What do the last 20-30 lines of the message log look like?
The last few lines said that all the updates had been applied correctly and all I had to do to finalize them was close FO3MasterUpdate.
Did you make any changes at all (activating/deactivating/moving of a module) to your load order between running FO3MasterUpdate and playing the game?
No.
Did you start with a savegame that was created by 1.4 or earlier?
No. I reinstalled when I bought Broken Steel, so I patched to 1.5 before playing.
Savegames with mods created by Patch 1.5 before you correctly ran FO3MasterUpdate are very likely already corrupted. You MUST revert to a pre-1.5 savegame.
I'm not quite sure what you mean there. Are you saying I have to install the mods and create a save BEFORE patching to 1.5?
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This was how I went about using FO3MasterUpdate.
Initially, I simply activated the mods I wanted and then ran it, but that made no difference.
So I uninstalled FO3 and all my DLCs (I have and use all 3), and deleted the FO3 directory on my HDD. I then reinstalled FO3, patched to 1.5, installed the DLCs, played the game's intro (Escape the Vault and then get to Megaton), installed my mods, set the load order with FOMM, backed up my DATA folder, then used FO3MasterUpdate. After that, still nothing worked.