Do you have any flags go with your F@H folding? Like -advmethods and -forceasm stuff like that. I have found that the -advmethods limit you to get only the WUs from the new generation, which are fast folders, but also error contained. For more info you can check out standford F@H forum. For me, I just removed -advmethods from both of my machines two days ago, one got the Tinker core core 65, one got the 404pts core 78. Notice these cores are old and don't get corrupt anytime. The new core 7a (with -advmethods) which I used to fold with sometimes corrupted and I had to redownload and got on with the drill...
I'm currently folding those 2 cores 65 and 78, and it's taking quite long already (both over 1 day), should be finished by tomorrow (hopefully).
Did you try different IDE cable and different molex plug, I found that HD get quite sensitive if those things ain't working.
Thanks all and take care.