"I didn't see anything in the BIOS about it being disabled on OS startup" Such a setting does not exist. Have you given it sufficient time for Windows to load drivers for them (up to 10 minutes)?  You may need to get PS/2 adapters for your USB KVM (if your KVM supports them). Not all systems have a "legacy USB" option ... USB on the 2650 IS legacy (the 2650 shipped from Dell between 2002 and 2004) :)  Your only options in the BIOS is to enable or disable USB. I have had very mixed results using USB mouse/keyboard on a 2650 - in some cases the drivers are extremely slow to load, in some cases, they never do.
I have purchased 6 Dell Poweredge 2650s used.  Now I am not sure how they have it set up, but when the computer is in the boot up sequence I can use the keyboard and mouse to enter the BIOS, but when Windows Server 2000 on one and 2003 on the others boot up it shuts down the USB ports.  I am new to working with Servers and would appreciate any help with this.  I am thinking it has to be part of the previous owners settings and it could be something that is part of the BIOS.  Which from looking in there I didn't see anything where USB was disabled.
USB Failure on OS Start up Poweredge 2650