This thread has some good information in it as I am experiencing similar issues since moving from RC.
I have an ATEN MasterView CS-1744 KVM hooked to my Nvidia GF 8500 GT . I went through drivers/firmwares/BIOS updates, but the issue remains. Upon returning the KVM to the Win 7 machine, one monitor gets 'lost'. The quickest 'fix' for this issue when it occurs is to hit 'Win+P' (Windows Key + P) to bring up the projector menu. Selecting 'Extend' (it is already selected for me) and hitting 'Enter' miraculously brings my second monitor back.
EDIT: This is definitely driver related for me. I was having other issues with Windows 7 x64, so I formatted and installed Win7 x32. I noticed right away that this issue was gone, then during the windows update process, it came back. I tried a myriad of solutions, and one solved it. Rolling back my video card drivers. This removed the NVIDIA Control Panel and now both of my monitors are there when I use my KVM