I have these occur about every third or so launches. Its not always the same mod, but it's always a .cfg file being open. and No I don't have any files open, it happens on a dedicated server as well as single player. Most of the time I just re-launch, but sometimes it can happen 3 or 4 time in a row.
http://pastebin.com/zGK6B4WF
http://pastebin.com/eZTgib6t
http://pastebin.com/FCXP8Xqp