I've been running a couple of tests with the Windows 7 logo kit, and one 
warning that's coming up in the report looks like this:

Test case: Remove all non-shared files and folders.: PASS WITH WARNINGS
WARNING: This application failed to remove the following files during uninstall:
File 
C:\Windows\winsxs\x86_microsoft.vc80.atl_1fc8b3b9a1e18e3b_8.0.50727.762_none_11ecb0ab9b2caf3c\ATL80.dll
 from program iceManager Monitor was not deleted.
File 
C:\Windows\winsxs\x86_microsoft.vc80.mfc_1fc8b3b9a1e18e3b_8.0.50727.762_none_0c178a139ee2a7ed\mfc80.dll
 from program iceManager Monitor was not deleted.
(there were more files, but you get the idea)

In my installer, I install the MFC and ATL merge modules with this markup:

<Merge Id="CRT8" Language="1033" DiskId="1" 
SourceFile="$(env.CommonProgramFiles)\Merge 
Modules\Microsoft_VC80_CRT_x86.msm"/>
<Merge Id="MFC8" Language="1033" DiskId="1" 
SourceFile="$(env.CommonProgramFiles)\Merge 
Modules\Microsoft_VC80_MFC_x86.msm"/>
<Merge Id="ATL8" Language="1033" DiskId="1" 
SourceFile="$(env.CommonProgramFiles)\Merge 
Modules\Microsoft_VC80_ATL_x86.msm"/>

. . .
<MergeRef Id="CRT8"/>
<MergeRef Id="MFC8"/>
<MergeRef Id="ATL8"/>

Everything works just fine, but is there a reason why the merge modules aren't 
uninstalled with the application?  I dug around a little, and it doesn't look 
like there's anything that tries to flag them as permanent, and I haven't come 
across anything useful in the logs yet, but I thought I'd check to see if this 
was a known issue (in general or with these MSMs in particular), or if there 
was a known workaround.

Thanks for the help!

Chris
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