Drive consistency preventing boot problem

Hi
Having installed a new drive ( NTFS ) to my system running Win2000 the
existing drive ( FAT32 ) is checked for consistency every time I boot, it
then reboots itself on completion ( Drive OK ) and checks again etc...
I can only boot in safe mode.
Have run virus check ( current ) and is ok.

Should I reformatt the NTFS drive to FAT32 ?
Is it possible that deleted files from the NTFS drive in the recycle bin on
the FAT32 drive are giving this problem?

Thanks if you can help

Simon