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Start menu icons not displaying correctly

I have repackaged an .exe into and .msi using repackager. If I open the .msi in Editor or Tuner the icons show up correctly. However when I run the .msi on a test machine running Win7 64-bit the icons are replaced with generic application or bat file icons instead of the ones created by the developer. The icons display correctly when you browse to their actual location stored under Program Files (x86). Does any one know why this might be happening?
(4) Replies
Are the icons in a separate file with the same extension as the file the shortcut targets?

MyAppIcons.exe for shortcut which targets MyApp.exe

You might want to look at the two paragraphs under Remarks at this link.
Yes. It is an app intended for 64 bit machines but its built as a 32 bit app. I have been running repackager on a 64 test box and am wondering now if some files are getting misplaced. I am going to try to run repackager on a 32 bit machine to see if that makes any difference.
Best Practice is to repackage32bit Apps on a 32bit OS and 64bit Apps ona 64bit platform.

Even if your target OS is Always 64bit..!
Agreed. We were able to solve the issue. When the .msi was installing, it was creating the icon files for the shortcuts, but it was placing them in the TEMP folder. Once the install finished these files were being deleted and thus when you went to open the application the icons were being replaced with generic windows ones since the originals no longer existed in the temp folder. The solution was to grab the icon files with a third party app, create our own icon files and have them install in the Program Files folder. We then edited the .msi so it looked for those new files in the new location. Thank you for the input.