This is definitely not a comed bug, or any sauerbraten bug in the case of "zooakakadoo and the missing files". First thing that comes to mind, might be an antivirus program automatically deleting it. You might wanna check those logs for confirmation. Otherwise, except of you accidently moving the files (drag'n'droppish) to somewhere else, there isn't really anything I can think about, but a hardware fault. Yes, even new hardware can be broken.
In the case of the crash when mapping, I suspect again an Intel/AMD chipset, because you mentioned the crashes even happen with the vanilla client. If you've got Intel, my understanding is, you are fucked. In the case of AMD, you might get lucky with another driver version.