I have a Visual Studio 2013 solution that is under source control (TFS, Visual Studio Online). It is mapped to a local workspace, I have checked out some files (e.g. web.config,
It turns out this was caused by disk encryption software. Disabling the disk encryption software services each time after starting VS2013 solves the problem. I did not have this problem with earlier versions of Visual Studio, presumably because of the new copy-replace cycle adopted by VS2013 mentioned in EDIT 2 in my original question.
Apologies for not coming back to comment and answer my original question, I completely forgot about it.