Hi,
Does the KVM switch interface with the software in any way? My understanding is that they simply switch the Keyboard, Mouse, and Video connections. This alone shouldn't cause any more problems in Linux than it would in Windows, unless the KVM switch talks to software on the computer (maybe through USB?).
Instead it would seem to me that you have some other problem causing Linux to not boot. Does it say anything before it freezes? Or do you just get a blank screen? If you have both OSes installed on the same hard drive, it could be a LILO problem (assuming you are using LILO as your bootloader).
-Nick