Hello,
I have the same issue. I double-checked that .NET package is marked as
permanent and I tried both with and without rollback boundary but I still
get ARP entry right after .NET is installed as prerequisite. I'm using Wix
3.9.

My Chain is defined this way:
<Chain>
  <PackageGroupRef Id="NetFx45Redist"/>
  <RollbackBoundary />
  <PackageGroupRef Id="TestPackage" />
</Chain>

The log from initial run is this:

[0690:0168][2015-07-08T00:29:07]i001: Burn v3.9.1006.0, Windows v6.1 (Build
7601: Service Pack 1), path:
C:\Users\Administrator\Desktop\TestInstaller.exe, cmdline: '-burn.unelevated
BurnPipe.{4303C9F0-DB96-41D1-A217-26466A0A9178}
{253C2727-CA99-43F7-B8B1-CF0835E221F0} 380 '
... snip ...
[0690:0168][2015-07-08T00:29:07]i000: Loading prerequisite bootstrapper
application because managed host could not be loaded, error: 0x80070490.
[0690:0464][2015-07-08T00:29:07]i000: Setting version variable
'WixBundleFileVersion' to value '1.0.0.0'
[0690:0168][2015-07-08T00:29:07]i100: Detect begin, 2 packages
[0690:0168][2015-07-08T00:29:07]i000: Registry key not found. Key =
'SOFTWARE\Microsoft\NET Framework Setup\NDP\v4\Full'
[0690:0168][2015-07-08T00:29:07]i052: Condition 'PreviousInstallFolder'
evaluates to false.
[0690:0168][2015-07-08T00:29:07]i052: Condition 'NETFRAMEWORK45 >= 378389'
evaluates to false.
[0690:0168][2015-07-08T00:29:07]i101: Detected package: NetFx45Redist,
state: Absent, cached: None
[0690:0168][2015-07-08T00:29:07]i101: Detected package: TestPackage, state:
Absent, cached: None
[0690:0168][2015-07-08T00:29:07]i199: Detect complete, result: 0x0
[0690:0168][2015-07-08T00:29:09]i200: Plan begin, 2 packages, action:
Install
[0690:0168][2015-07-08T00:29:09]w321: Skipping dependency registration on
package with no dependency providers: NetFx45Redist
[0690:0168][2015-07-08T00:29:09]i000: Setting string variable
'NetFx45FullLog' to value
'C:\Users\ADMINI~1\AppData\Local\Temp\TestInstaller_20150708002907_0_NetFx45Redist.log'
[0690:0168][2015-07-08T00:29:09]i201: Planned package: NetFx45Redist, state:
Absent, default requested: Present, ba requested: Present, execute: Install,
rollback: None, cache: Yes, uncache: No, dependency: None
[0690:0168][2015-07-08T00:29:09]i201: Planned package: TestPackage, state:
Absent, default requested: Absent, ba requested: None, execute: None,
rollback: None, cache: No, uncache: No, dependency: None
[0690:0168][2015-07-08T00:29:09]i299: Plan complete, result: 0x0
[0690:0168][2015-07-08T00:29:09]i300: Apply begin
[017C:054C][2015-07-08T00:29:09]i360: Creating a system restore point.
[017C:054C][2015-07-08T00:29:09]i362: System restore disabled, system
restore point not created.
[017C:054C][2015-07-08T00:29:09]i000: Caching bundle from:
'C:\Users\ADMINI~1\AppData\Local\Temp\{380d557e-ec88-4923-9924-a37299972102}\.be\TestInstaller.exe'
to: 'C:\ProgramData\Package
Cache\{380d557e-ec88-4923-9924-a37299972102}\TestInstaller.exe'
[017C:054C][2015-07-08T00:29:09]i320: Registering bundle dependency
provider: {380d557e-ec88-4923-9924-a37299972102}, version: 1.0.0.0
[017C:0504][2015-07-08T00:29:09]i305: Verified acquired payload:
NetFx45Redist at path: C:\ProgramData\Package
Cache\.unverified\NetFx45Redist, moving to: C:\ProgramData\Package
Cache\CD57380514DC157DF75A09D3E54C96D1DF3DF51A\redist\dotnetfx45_full_x86_x64.exe.
[017C:054C][2015-07-08T00:29:09]i301: Applying execute package:
NetFx45Redist, action: Install, path: C:\ProgramData\Package
Cache\CD57380514DC157DF75A09D3E54C96D1DF3DF51A\redist\dotnetfx45_full_x86_x64.exe,
arguments: '"C:\ProgramData\Package
Cache\CD57380514DC157DF75A09D3E54C96D1DF3DF51A\redist\dotnetfx45_full_x86_x64.exe"
/q /norestart /ChainingPackage "Test Installer" /log
"C:\Users\ADMINI~1\AppData\Local\Temp\TestInstaller_20150708002907_0_NetFx45Redist.log.html"'
[0690:0168][2015-07-08T00:33:20]i319: Applied execute package:
NetFx45Redist, result: 0x0, restart: None
[0690:0168][2015-07-08T00:33:20]i399: Apply complete, result: 0x0, restart:
None, ba requested restart:  No
[0690:0168][2015-07-08T00:33:20]i500: Shutting down, exit code: 0x0
[0690:0168][2015-07-08T00:33:20]i000: The prerequisites were successfully
installed. The bootstrapper application will be reloaded.
[0690:0168][2015-07-08T00:33:20]i006: Bootstrapper application requested to
be reloaded.
[0690:0168][2015-07-08T00:33:20]i000: Loading managed bootstrapper
application.
[0690:0168][2015-07-08T00:33:20]i000: Creating BA thread to run
asynchronously.
[0690:060C][2015-07-08T00:33:20]i000: Starting Bootstrapper. Assembly
CodeBase:file:///C:/Users/Administrator/AppData/Local/Temp/{380d557e-ec88-4923-9924-a37299972102}/.ba1/TestInstaller.DLL
[0690:060C][2015-07-08T00:33:20]i000: Command Action: Install Resume: None
Restart: Prompt Display: Full LayoutDir:  Passthrough: False Relation: None
... snip ...
[0690:060C][2015-07-08T00:33:50]i000: Exiting UI.
[0690:0168][2015-07-08T00:33:50]i500: Shutting down, exit code: 0xffffffff
[0690:0168][2015-07-08T00:33:50]i000: Shutting down without restart.
... snip ...
[0690:0168][2015-07-08T00:33:50]i007: Exit code: 0xffffffff, restarting: No




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