I think there is an issue with Merge Modules/WixLibs/product.wxs... Wixlibs 
require you have a directory element in each wixlib that is the same
Then in the merge module I reference that wixlib directory 

The wixlibs has the directory element as such (same for each wixlib):

<ComponentGroup Id="cmpgrp_TitusSharedDataDlls" 
Directory="WixLibRedirectFolder">

Each of my merge modules are now:

<Directory Id="TARGETDIR" Name="SourceDir">
        <Directory Id="WixLibRedirectFolder">

Then in the product.wxs each merge module is:

<Directory Id="ProgramFilesFolder" DiskId="1">
        <Directory Id="INSTALLFOLDER" Name="TITUS" DiskId="1">
          <Directory Id="DIRECTORY_PATH_SERVICES" Name="TITUS Services" 
DiskId="1">

            <Directory Id="AUDITLOG_SERVICE" Name="EnterpriseAuditLogService" 
DiskId="1">
              <Merge Id="EnterpriseAuditLogServicesMM" DiskId="1" 
SourceFile="$(var.SolutionDir)..\wixlib\TitusEnterpriseAuditLogServicesMergeModule.msm"
 Language="1033"/>
            </Directory>

            <Directory Id="MANAGEMENT_SERVICE" 
Name="EnterpriseManagementService" DiskId="1">
              <Merge Id="EnterpriseManagementServicesMM" DiskId="1" 
SourceFile="$(var.SolutionDir)..\wixlib\TitusEnterpriseManagementServicesMergeModule.msm"
 Language="1033"/>
            </Directory>

Etc...

The logfile for the REPAIR has set the WixLibRederictFolder to the same path:

MSI (s) (18:E0) [13:28:00:027]: PROPERTY CHANGE: Adding TARGETDIR property. Its 
value is 'C:\'.
MSI (s) (18:E0) [13:28:00:027]: PROPERTY CHANGE: Adding INSTALLFOLDER property. 
Its value is 'C:\Program Files\TITUS\'.
MSI (s) (18:E0) [13:28:00:027]: PROPERTY CHANGE: Adding DIRECTORY_PATH_SERVICES 
property. Its value is 'C:\Program Files\TITUS\TITUS Services\'.
MSI (s) (18:E0) [13:28:00:027]: PROPERTY CHANGE: Adding COMMON_SERVICE 
property. Its value is 'C:\Program Files\TITUS\TITUS Services\Common\'.
MSI (s) (18:E0) [13:28:00:027]: PROPERTY CHANGE: Modifying 
WixLibRedirectFolder.CA23A0DC_B2DE_4F2C_9E74_FD373F99E9D7 property. Its current 
value is 'C:\Program Files\TITUS\TITUS Services\Common'. Its new value: 
'C:\Program Files\TITUS\TITUS Services\Common\'.
MSI (s) (18:E0) [13:28:00:027]: PROPERTY CHANGE: Adding SETTINGS_SERVICE 
property. Its value is 'C:\Program Files\TITUS\TITUS 
Services\EnterpriseSettingsService\'.
MSI (s) (18:E0) [13:28:00:027]: PROPERTY CHANGE: Modifying 
WixLibRedirectFolder.A54690A6_C7B5_477D_ADAF_916A4A173FDF property. Its current 
value is 'C:\Program Files\TITUS\TITUS Services\EnterpriseSettingsService'. Its 
new value: 'C:\Program Files\TITUS\TITUS Services\EnterpriseSettingsService\'.
MSI (s) (18:E0) [13:28:00:027]: PROPERTY CHANGE: Adding POLICY_SERVICE 
property. Its value is 'C:\Program Files\TITUS\TITUS 
Services\EnterprisePolicyService\'.
MSI (s) (18:E0) [13:28:00:027]: PROPERTY CHANGE: Modifying 
WixLibRedirectFolder.21C4128B_7484_4589_ABC5_E3FA2A95D2B6 property. Its current 
value is 'C:\Program Files\TITUS\TITUS Services\EnterpriseSettingsService'. Its 
new value: 'C:\Program Files\TITUS\TITUS Services\EnterpriseSettingsService\'.
MSI (s) (18:E0) [13:28:00:027]: PROPERTY CHANGE: Adding MANAGMENT_SERVICE 
property. Its value is 'C:\Program Files\TITUS\TITUS 
Services\EnterpriseManagementService\'.
MSI (s) (18:E0) [13:28:00:027]: PROPERTY CHANGE: Modifying 
WixLibRedirectFolder.D40E1FBB_05DF_4124_9CBB_3C09B6004B44 property. Its current 
value is 'C:\Program Files\TITUS\TITUS Services\EnterpriseSettingsService'. Its 
new value: 'C:\Program Files\TITUS\TITUS Services\EnterpriseSettingsService\'.
MSI (s) (18:E0) [13:28:00:027]: PROPERTY CHANGE: Adding AUDITLOG_SERVICE 
property. Its value is 'C:\Program Files\TITUS\TITUS 
Services\EnterpriseAuditLogService\'.
MSI (s) (18:E0) [13:28:00:027]: PROPERTY CHANGE: Modifying 
WixLibRedirectFolder.9EFC3F5B_3D47_4233_A162_371DEF5D8E92 property. Its current 
value is 'C:\Program Files\TITUS\TITUS Services\EnterpriseSettingsService'. Its 
new value: 'C:\Program Files\TITUS\TITUS Services\EnterpriseSettingsService\'.
MSI (s) (18:E0) [13:28:00:027]: PROPERTY CHANGE: Modifying 
DIRECTORY_PATH_PROGRAMDATA property. Its current value is 
'C:\ProgramData\TITUS'. Its new value: 'C:\ProgramData\TITUS\'.
MSI (s) (18:E0) [13:28:00:027]: Target path resolution complete. Dumping 
Directory table...
MSI (s) (18:E0) [13:28:00:027]: Note: target paths subject to change (via 
custom actions or browsing)
MSI (s) (18:E0) [13:28:00:027]: Dir (target): Key: TARGETDIR    , Object: C:\
MSI (s) (18:E0) [13:28:00:027]: Dir (target): Key: ProgramFiles64Folder , 
Object: C:\Program Files\
MSI (s) (18:E0) [13:28:00:027]: Dir (target): Key: INSTALLFOLDER        , 
Object: C:\Program Files\TITUS\
MSI (s) (18:E0) [13:28:00:027]: Dir (target): Key: DIRECTORY_PATH_SERVICES      
, Object: C:\Program Files\TITUS\TITUS Services\
MSI (s) (18:E0) [13:28:00:027]: Dir (target): Key: COMMON_SERVICE       , 
Object: C:\Program Files\TITUS\TITUS Services\Common\
MSI (s) (18:E0) [13:28:00:027]: Dir (target): Key: 
WixLibRedirectFolder.CA23A0DC_B2DE_4F2C_9E74_FD373F99E9D7    , Object: 
C:\Program Files\TITUS\TITUS Services\Common\
MSI (s) (18:E0) [13:28:00:027]: Dir (target): Key: SETTINGS_SERVICE     , 
Object: C:\Program Files\TITUS\TITUS Services\EnterpriseSettingsService\
MSI (s) (18:E0) [13:28:00:027]: Dir (target): Key: 
WixLibRedirectFolder.A54690A6_C7B5_477D_ADAF_916A4A173FDF    , Object: 
C:\Program Files\TITUS\TITUS Services\EnterpriseSettingsService\
MSI (s) (18:E0) [13:28:00:027]: Dir (target): Key: POLICY_SERVICE       , 
Object: C:\Program Files\TITUS\TITUS Services\EnterprisePolicyService\
MSI (s) (18:E0) [13:28:00:027]: Dir (target): Key: 
WixLibRedirectFolder.21C4128B_7484_4589_ABC5_E3FA2A95D2B6    , Object: 
C:\Program Files\TITUS\TITUS Services\EnterpriseSettingsService\
MSI (s) (18:E0) [13:28:00:027]: Dir (target): Key: MANAGMENT_SERVICE    , 
Object: C:\Program Files\TITUS\TITUS Services\EnterpriseManagementService\
MSI (s) (18:E0) [13:28:00:027]: Dir (target): Key: 
WixLibRedirectFolder.D40E1FBB_05DF_4124_9CBB_3C09B6004B44    , Object: 
C:\Program Files\TITUS\TITUS Services\EnterpriseSettingsService\
MSI (s) (18:E0) [13:28:00:027]: Dir (target): Key: AUDITLOG_SERVICE     , 
Object: C:\Program Files\TITUS\TITUS Services\EnterpriseAuditLogService\
MSI (s) (18:E0) [13:28:00:027]: Dir (target): Key: 
WixLibRedirectFolder.9EFC3F5B_3D47_4233_A162_371DEF5D8E92    , Object: 
C:\Program Files\TITUS\TITUS Services\EnterpriseSettingsService\
MSI (s) (18:E0) [13:28:00:027]: Dir (target): Key: DIRECTORY_PATH_PROGRAMDATA   
, Object: C:\ProgramData\TITUS\

-----Original Message-----
From: Rob Mensching [mailto:r...@robmensching.com] 
Sent: January-31-13 9:43 AM
To: General discussion for Windows Installer XML toolset.
Subject: ** SPAM **[WiX-users] [SPAM] Re: When doing a REPAIR, all files are 
going into 1 folder instead of the specific folders...

John, you shouldn't have to preserve Directory paths if a Component is 
installed in it. You do need to preserve any Property values that you want 
persisted.

Steve, sorry, I usually point people to the verbose log file to help them jump 
start their investigation. I unfortunately don't have time to root cause all 
the issues people post here from scratch.


On Thu, Jan 31, 2013 at 6:22 AM, John Cooper <jocoo...@jackhenry.com> wrote:

> Chances are really good that you're not correctly preserving the 
> complete directory tree where those files are going.  In many ways, a 
> patch is just a repair on one feature.  The Windows Installer Service 
> has no memory of your whole directory tree.  Generally, you have to 
> preserve things like INSTALLLOCATION or INSTALLFOLDER in your registry 
> and recovery them using a registry search for repair and patch to work 
> properly.
>
> --
> John Merryweather Cooper
> Build & Install Engineer - ESA
> Jack Henry & Associates, Inc.®
> Shawnee Mission, KS  66227
> Office:  913-341-3434 x791011
> jocoo...@jackhenry.com
> www.jackhenry.com
>
>
>
>
> -----Original Message-----
> From: StevenOgilvie [mailto:sogil...@msn.com]
> Sent: Thursday, January 31, 2013 8:04 AM
> To: wix-users@lists.sourceforge.net
> Subject: Re: [WiX-users] When doing a REPAIR, all files are going into 
> 1 folder instead of the specific folders...
>
> Any idea Rob?
>
>
>
> --
> View this message in context:
> http://windows-installer-xml-wix-toolset.687559.n2.nabble.com/Weird-Re
> pair-happening-tp7583229p7583292.html
> Sent from the wix-users mailing list archive at Nabble.com.
>
>
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