It's not obviously possible that installing our software would "revert" your FS9.1 to 9.0, we surely are not including any of the original files from Microsoft in our installer.
A common mistake FS9 users do who are convinced to have installed 9.1 ( because they installed the 9.1 patch ), is to later on install a NOCD crack made for FS9.0, which creates a mixedup version, because you have all the .DLLs from 9.1 ( I'm assuing you had installed the patch), but the .EXE from 9.0, because it was replaced by the NOCD.
So, if you use a NOCD, be absolutely sure it's for 9.1. I assume the window that says "FS9 9.0 has stopped working" it's the normal Windows error report dialog so, clearly, you DO have 9.0, at least the .EXE is.