OK, I'll try to help. but I am only a amatur at this.
If the drive was working fine before this, its probably not the connections on the cables, but you might want to chack anyway.
Now, for some questions-
Is the drive partitioned in any way, or is it just one big drive?
If your pretty sure that you have eliminated virus/spyware as reasons, and the drive is working part of the time, you could have a bad drive. I've heard of them failing this fast before.
You best bet is probably to back everything that is on it somewhere else, and then reformat the whole thing. If the same problems keep happening after a format, your drive is probably busted. You might want to chack and see if you have a warrenty on the drive. I know most companies have a 1 year policy for hard drives.
There are a good deal of tech people on these forums, you might want to wait and see what the rest have to say.