I've recently had a drive get so fragmented it would cease to function altogether; it was being reported as having very little fragmentation only to find out, by running a better defrag, it was actually extremely fragmented.
It's because of that and experiences like yours that I now stick to the top-rated defrag. Prior to this I never suspected this was even possible so it was a long frustrating discovery for me.
There are some other good suggestions by the prior posters but you may want to completely rule out this possibility in your SQL also.
Here's a link to a FREE DEFRAG TRIAL[/url] for the product I used. If it's not the version you need you could contact them to see if there is a trial available for the version you might require. This is a rare problem as far as I know but, at the same time, if it is what is happening to your SQL it must be ruled out 100% because doing other things may make it worse.
Hope this helps