by Steve Gallagher.
Just thought I would comment on this. We did determine the problem in the end. The drive hosting the moodledata folder had run out of space. The database side of things (replication notwithstanding) was fine and the permissions were fine.
In the end the problem revealed itself from the apache errorlog. A df and a du and an rm -fv of a backup directory and the problem was solved.
I suspect this was also why the original upgrade failed as well.
Thanks for the description of how the file upload worked. That helped narrow the problem.