HD's go bad
I'm almost certain it has nothing to do with cables and/or connections. More
likely, you have some program trashing system memory. Specially if you're using
a disk cache. As far as the controller goes, if it has its own cache, there is
a chance it could be getting screwed up but it's by far a less likely scenario.
Run the system with a clean setup for a while and see if that continues to
happen.