The location of the exes is taken from the registry and put in $(WixToolPath). 
Can you check the InstallRoot value under
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows Installer XML\3.5
or
HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows Installer XML\3.5
and see if it is correct?
Otherwise, are you overriding $(WixToolPath) somewhere else in the project?

Pete


----------------------------------------
> Date: Wed, 1 Feb 2012 22:56:52 +0000
> From: mark.sug...@gmail.com
> To: wix-users@lists.sourceforge.net
> Subject: Re: [WiX-users] Install issue - wix2010.target line 761
>
> Thanks for the reply.
>
> How do I set %WIX%? And what should I set it to?
>
> Previously, I just installed WiX and compile worked fine. What might
> have changed?
>
> On Wed, Feb 1, 2012 at 18:05, Blair <os...@live.com> wrote:
> > I don't know. Is the %WIX% environment variable set?
> >
> > I use the HarvestDirectory items instead of the PreBuildEvent property to
> > use the harvester in 3.5 myself.
> >
> > -----Original Message-----
> > From: Mark Sugrue [mailto:mark.sug...@gmail.com]
> > Sent: Wednesday, February 01, 2012 8:57 AM
> > To: wix-users@lists.sourceforge.net
> > Subject: [WiX-users] Install issue - wix2010.target line 761
> >
> > I'm setting up a new build machine. VS2010, Wix3.5, etc. Everything the same
> > as the old machine. (both are x64 Win7 Pro)
> >
> > When I try to build the installer on the new machine, I get an odd error
> > which I don't understand. Nothing on the web seems to match it.
> >
> > The error isn't in my code, its on line 761 of wix2010.targets
> >
> > The line is <Exec WorkingDirectory="$(OutDir)"
> > Command="$(ExpandedPreBuildEvent)" />
> >
> > I haven't edited this file at all.
> >
> > The error I get is this:
> >
> > Error   3       The command ""%WIX%\bin\heat" dir
> > "D:\Code\products\LE\bin\Debug\Help" -dr HelpFolder -cg HelpComponentGroup
> > -var var.HelpDir -srd -gg -sfrag -suid -template:fragment -out
> > "D:\Code\products\LE\Setup\help.wxs.sample""
> > exited with code 3.     C:\Program Files
> > (x86)\MSBuild\Microsoft\WiX\v3.x\wix2010.targets        761     6
> > Setup
> >
> > But the exact same code compiles fine on the old machine.
> >
> > Is there some setting I need to change maybe?
> >
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