So I've been tracking a problem for about a month now, that sometimes drives would stop working, would "disconnect" and everything would halt. I've tried everything, even replacing a harddrive after eliminating it was about the only thing that could be wrong.
In the end, after countless hours of testing, fiddling and cursing, it was the SATA cables and also the Intel RST 10.6 drivers. Both of which I installed not long before the problems started. The drivers made sure my SSD boot disk acted funny or not at all sometimes. The SATA cables gave me other problems: unexpectedly a hard drive would become inaccessible. This gave problems in Windows because sometimes it was waiting for the data and it didn't come, so it hanged.
I've only recently come to the conclusion that it was the cables and not the motherboard, because I bought a dual-port SATA600 PCI-express card and I used those wretched Belkin angle cables, after an hour it again stopped copying files and the drive was inaccessible. After replacing the cables, it has copied over 2TB of data without a single problem.
Belkin SATA cables, you cost me countless hours of frustration. You will burn in hell for your crimes.