Simultaneous volume failing

Hi, I have 2 Seagate FreeAgent GoFlex 1.5TBs. Recently, one of the partitions on one (I'll refer to it as the first one) won't show up in Finder, but still would show up in Disk Utility (although grayed out). Therefore, I hit "Repair Disk", and it shows, "Disk Utility can't repair this disk. Backup as many of your files as possible, reformat the disk and restore your backed-up files.", and somehow opens it in Finder. So I moved the content of that partition to a partition in disk #2. In the process, I saw a virus alert (Sophos) for some variant of the Blackhole exploit kit (I don't remember the exact name. That was one of the files I've backed up from a Windows computer.), and I removed it. (I don't know whether or not this is relevant.)  Then, I formatted the failed partition, created a new partiton, and replaced all of my files.
A few days later, I went to use the mentioned partition on disk #1, and saw that the same thing happened. So therefore I went to use the mentioned partition in disk #2. It has also failed. Keep in mind that I've forgot to clean off the files from the partition on disk#1 that were on the partition on disk#2. I have the feeling that it is because of a file from disk#1 that perhaps corrupted the disk, but I don't know
Does anyone here have any guess to why, and how I can fix both of the partitions?

Sounds to me like that drive is failing, which will destroy both partitions at the same time. If you have any data on that drive that isn't backed up anywhere else, get it off there ASAP!
This is definitely not related to that Blackhole file. Blackhole is currently not able to infect an up-to-date Mac system, and a file can't corrupt a volume simply by being copied to it.

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