To stop it from happening, go to the start menu, hit run, type in "cmd" (Excluding the quotation marks) and type in
chkntfs /x c:
assuming C is your main hard drive, and the only hard drive that it's preforming CHKDSK on. If you have multiple drives, and it's preforming it on all of them, just add them in, so it looks like:
chkntfs /x c: d:
Hope it helps.