So it seems Garry 'fixed' something by making server.cfg load before the Lua engine does, or at least before UPPL does.
Makes sense, but it causes havoc if used to setting lua commands in server.cfg
If using ULX, you may wish to copy addons/ulx/cfg/server.ini to your gmod/cfg, edit it from within gmod/cfg, add one line to it's end; ulx exec <filename> where file name is...
take all the uppl commands out of your server.cfg, put them in a text file named <filename>.cfg in your gmod/cfg folder.
(I recommend uppl.cfg, obvious, no?)
As for if you don't run ULX, wellll, uh... I can't think of another easy way at the moment.