Fixed in pull #297 to develop around January 21, 2014. This should also be in release/2.9 as well although I believe it was pulled into 2.9 a week or so later.
Re: Glitch when saving an edited file after timing outby Michael Gage - Number of replies: 0
This is a known bug. http://bugs.webwork.maa.org/show_bug.cgi?id=2989