Win 2000 in Setup Loop

A dual boot pc (Win2000/win98) suddenly unable to boot into Win2k. (98 ok). Each time a boot into 2k is attempted the system tries to run “Setup”.It asks for the CD and if provided it will run setup for a time and then do a restart. The whole process then again. Even if I try to get into Safe Mode it will start set-up.
I cannot get a command prompt because it also goes into a set-up!
Anyideas as to the cause? Customer is very anxious not to lose his data otherwise I would simply format and reinstall!