Sounds like you need an updated HotSync software package, version 3.1.1 or higher. Information on 3.1.1 is here:
http://www.palm.com/support/downloads/palmhs_update.html

And specificially it talks about the changes to Windows 2000 IR, and that 3.1.1 is updated to address these changes.

IR in 2000 dosen't let you just set a com port like 98 did.