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MS VC++ 2008 manifest problems

I did a clean install to Windows Vista and downloaded the latest VC++ 2008. It gave me an error every time I wanted to run my application:
"The application has failed to start because its side-by-side configuration is in
correct. Please see the application event log for more detail."

What I did was go into the output directory myapp/Debug and delete all the files, then rebuild. I did this for all the project dependencies that I had source access to as well. This worked for me, although who knows what else could have been going wrong.