I got a disc failure. Luckily the server has a RAID, so no imminent data loss occurred. However, it is a RAID-5 setup, so the system performance was impacted heavily.
Now I transferred the entire system into Microsoft Azure and it seems to be running little bit better. The project was a huge one and I had to tinker with it a lot. I guess I'll have to do a full discosure about that later.
Hopefully this thing stays working this time.