Try invoking the 4GBFNV patcher with just "-laaexe" as the argument. I have used this method since MO version 1.3.4 and it works just fine for me.
All this is doing is removing the explicit placement of the patched exe and allowing the patcher to place it where it wants to. If you check with explorer afterwards you should find it in the 'exes' folder.
I doubt you will see any difference if you downgrade your MO to any version before this as there is nothing significant that has changed in the code used to call the executables. If you are having issues with 1.3.8 you will have them with 1.3.x.
I would still like to see your logs, not just snippets. Clear out the logs folder and start the game via the patcher in MO and either post them to a service like PasteBin or put spoiler tags around them and post them here.