Scandisk Kills Win2K

We have had serveral PC running Win2k start the scandisk at bootup. Scandisk deletes many files and the OS will not start up again. This is growing into a chronic problem. We do some imaging but a few of the machines have scandisked themselve to death running a CD install..... Has anyone else seen this? is there a fix? Mostly this happens when a removal of a software product trigers a scandisk. We also have scheduled a scandisk and it will restart and then delete the files. All machines are newer IBM pc's and it only happens on Win2K. All other OS's no problem...Thanks for any help....Chuck