This is standard behavior for the BES Clients.
The Older BES Clients will talk to a Newer BES Server.
The Newer BES Clients will talk to an Older BES Server.
Within limits. IBM seems to go to great lengths to ensure backwards and forwards compatibility of the clients.
Given that Win2003 is no longer publicly supported by Microsoft, it seems reasonable for IBM to drop support for it with their newer clients. In fact, I believe that is their policy. Once they begin to support an OS, they do so until the publisher stops supporting it.
Given that there are no new publicly available patches for Win2003 (or WinXP, Win NT, Win98, or Win95), you should be migrating OFF of Windows 2003 servers.
EDIT: That all said, I still have several hundred "unsupported" Operating systems in my environment. Linux, Windows, and Mac. Because the older clients still talk to the newer BES Server, we at least know what's out there and can perform basic management functions on them. We can't take advantage of all the newer features of the BigFix product, but the features that used to work, still do!