I am not sure if he ran Malewarebytes in safe mode, I know he ran Avast in safe mode.
It is looking like it was a false positive. I didn't realize that he ran Avast with everything turned to "high" ("heuristics" or something) so it was saying all sorts of stuff was possible problems.
Last night the computer seemed fine, and the various anti-virus scans he did on "normal" settings all came through okay. My son is paranoid about his computer getting infected, so whenever anything seems odd he gets all worked up.
Thanks for the responses!