Win 2k dual boot /OS/2 boot manager

I am dual booted with NT and 2000 using os/2 boot manager and everytime I go to the 2000 side it will erase my boot manager and then give me a blue screen of nothing when I reboot. Is there a way to eliminate file checking in the boot ini file of 2000 or a fix that will get 2000 not to view the boot manager partition?