Hi Sam,
There shouldn't be any problem with integrating the F5 Management Pack with Windows 2003 / SCOM RMS-clustering.
We used Windows 2008 R2 and SCOM 2007 R2 with our RMS-clustering installation instructions just for the simple fact that these are the latest platforms released by Microsoft, and we are striving to be compatible with the forefront technologies at hand. Most of the tests we've done with RMS-clustering were targeted against Windows Server 2008 and SCOM 2007 R2, but really the application programming interface used is backward compatible with Windows Server 2003 and SCOM 2007 SP1, as well.
This being said, I wouldn't worry about F5 Management Pack compatibility issues in supporting RMS-cluster on Windows Server 2003. Should any problems arise, just let us know and we'll do our best to assist you.
Thanks!
Julian