CHKDSK Runs on Boot Up- Have read sim threads no help

Hi
I run WinXP on two hard drives. A few weeks ago they suddenly started running chkdsk on every startup. Not for the boot partition but other partitions.. I put up with this for a while but eventually sought info on Google. I changed the Chkdsk service to the * one.
Which was supposed to cure. No effect.
I ran the dirty check and it said clean. So I gave up.
Eventually I started anticipating its arrival on the boot sequence and started clicking the
enter key to cancel it straight away. Suddenly it stopped happening. Great . A few days later I was doing something else, I think trying out Ubuntu 13.04 and when I rebooted to Win it started again. Today was the last straw. It came up and said "Hit any key in 60 seconds to cancel" I hit them repeatedly nearly needding a new keyboard. It blythely ignored me and proceeded to do its check. I rebooted and am running Ubuntu at this moment. I have in mind to delete the chkdsk chkdsk * entry and am enquiring if it will cause any other problem other than KILLING Chkdsk once and for all. Or is there some way I have missed which will cure this.
I thank any assistance I get in advance.