Request for chkdsk run on bootup which then hangs

hi

After transferring files from a fat32 external hdd my laptop now gives me a "one of your disks needs to be checked for consistency" message every time I boot up. If I allow it to run chkdsk automatically, it then hangs half way through. I have done a complete hardware check & all is clear. I have also found answers to similar problems for Vista thru regedit, but nothing for Windows 7 - help much appreciated! Graeme