Exibit has pointed out this has happened to him before, with a different hardware setup. It isn't related to the server HDD fault.Final thought : I do find it considerably co-incidental, that your issues started at the same time the server HD went corrupt. It could be ( unlikely I suppose, but I am looking at all possible scenarios ) that your downloading possibly corrupt custom map files/textures etc, which we as other users have no problems with, since se have already downloaded them to our clients prior to this, and your having issues with those now from the server. Could be nothing, but just worth considering. It might be worth rebuilding a test server from scratch which doesnt take long, to just make sure all our files are 100% ok. As there is not ( to my knowledge ) a method to verify the server files integrity, unlike the client which can be tested.
I could be wrong, but as I have said, just looking at all the options.
IXL
The other ideas are good, and it is a slow and exacting process of ruling out one thing at a time. First thing to do is re-install CSS and see if there is still a problem before trying out any other fixes.. It may just run fine after the full system re-install. Try Server1 tonight. If it doesn't work, then It may be a port problem, and this would be my first investigation. Let us know if the problem is still there, then we will cross the next bridge, a step at a time.
This may still turn out to be the cause of the more recent issue, and the re-install will prove that correct or otherwise.I think I may have deleted a file that was causing the auto kick