Probably not the operating system, unless the code is opening/closing files, and the namings are causing trouble. Usually filenaming is a backwards compatibility issue.
If the files are being pulled across a network, what is the OS of the network server?
Chances are it's the version of Excel. Excel's version conflicts usually halt the program; it doesn't continue on with flawed behavior.
Have you opened the offending workbooks and re-compiled them in the new version? What sort of compile errors do you see?
I have had issues toggling back and forth from the Excel 97 at work, and my home computer's Excel 2002. Usually Excel 97 does the complaining.