rfresh,
You shouldn't be deleting these older versions as some programs still rely on the older version due to the simple fact that version 3.xx was not out yet when they were developped. . They were built using lower version of Visual Basic or Visual Studio.
these are not all backward compatible.
As Celestra has pointed out, you need to repair them, not delete them.
This could be the exact reason you're getting the error messages.
If it wasn't that long ago and you haven't installed much software, I'd do a system restore.