FMP6 runs fine on Windows 7, but there are few things to pay attention to:
You may have to allow Filemaker access to the network (you'll get a dialog from W7)
If you are using plugins and push these from the server, the location of these plugins will
no longer be: "C:\Program Files\Filemaker\Filemaker Pro 6\System" (but this can still be used to place them "manually")
but will be: "C:\Users\<username>\AppData\Local\VirtualStore\Program Files\FileMaker\FileMaker Pro 6\System\"
I don't know how you access your IBM-data, but I guess that you use a ODBC-DSN. If you can create a identical DSN again on W7 it should be work fine.