I've reinstalled my Morrowind and am trying with the Python variant of the patch now .... if that makes a difference
There should be no difference, the Python and .exe version both apply the same binary patch to your Morrowind.exe.
... also are you using the MPP patch? I was told its a good choice to use but I cannot find it.
You can find the http://www.uesp.net/wiki/Tes3Mod:UMP.