Sounds like you're running a very resource tight system.
Mercury runs fine on such, provided you do not overuse RAM or have very little disk space left.
Periodically we purge the hidden windows update directories, and all the different temp directories that Windows uses. Via the scheduler we defrag every volume every night, and this is done after any backup is done, which also is done nightly. We do however only backup configurations and data, space would be impossible else.
The only case when Mercury could overuse the disk is by using up session log space, under heavy load. Be very careful about enabling session logging. Session logging is nearly the same as many others call debug logs, and they consume power as well as disk.
Tools we frequently use are:
SpinRite from Gibson Research CnW Recovery www.cnwrecovery.com
Filemon and TaskInfo
If ChkDsk solved your problem that was fine, but if you suspect any disk errors, you should first check the disk with diskmanager, then check the event log. If we still suspect disc-related problems, we run SpinRite (if it's not a RAid 1,5,6 unit), then lastly run chkdsk. However if you have mechanical errors on a disk, ChkDsk seriously damages the MFT and you will have real trouble getting your data back. You will notice problems with the mechanics if simple copy or ntbackup freezes. Then unplug the disk, insert into another computer and use CnW to read sector by sector to an image, and restore from that image whatever you can.
Best of luck