I support a mix of FM9, 10, and 11 clients & servers, and haven't noticed any significant issues.
Nothing major comes to mind. There were a few new bugs introduced you might want to look into to see if they affect behavior in any critical way in your system both of these are listed as "mac only" but I wouldn't be suprised to find that they also affect windows systems:
These are two of many acknowledged bugs that can be found in the Known Bug List here in the Report an Issue section of the forum.
It can also be downloaded as a database file from: http://www.4shared.com/file/8orL8apk/FMP_Bugs.html