It is possible that this may be related to Anti-Virus software doing something unexpected. Unfortunately I cannot provide much support in that area. One thing you can try though, would be to rebuild the Engine so that it works, then have your Anti-Virus software run a scan through the Unreal Engine folder to see if it throws up any false-positive results.
Have you noticed if this seems to be occurring at approximately the same time every day? For example, do you always notice the errors in the morning when you first try to build a project?