Ves - I suggest that you try with the pre-compiled binary in case your own version is not fully convergent with the master version.
Wormer - thank you for your feedback, that is helpful.
Dr. Supergood - the problem is probably inconsistencies in the number of threads between client and server for certain tasks where the number of threads should be the same - but, yes, if you have your number of threads changed from the default, you may well get desyncs until this issue is fixed.
Edit: I have also optimised the loading time considerably, which optimisation will be present in to-morrow's nightly build (the server will restart with this new build in a few hours). I should be interested to see whether this reduces the loading time on the server noticeably.