Repair of application (msi) fails but normal installation is successfull

asp.net,windows-installer,iis-6,repair

If you support 32 and 64-bit systems you need separate setups for both. http://blogs.msdn.com/b/heaths/archive/2008/01/15/different-packages-are-required-for-different-processor-architectures.aspx so you'd run the appropriate aspnet exe for the system, that might solve some problems. You haven't said if your setup is x86 or x64, so it's hard to say what the exact issue might be....