What version are you on?  I seem to recall there was a subtle bug that only showed up under certain (and rare) conditions where stuff like this would happen.  I also recall that it was mxd specific.  That is, if you open a fresh ArcMap session, everything behaves as it should.  Anyway, I'll check the support boards for this issue.  There's also a chance (!?!) the doc may be wrong, that a blank scratch workspace defaults to default.gdb.  
In the meantime... set your scratch workspace to your current workspace or another suitable known location.