One thing about adding and subtracting mods is that remnants of them are still in the Save folder, even if you did not Save a game. When the game starts the first time, it creates the SH4 folder in your C:\User \UserName \Documents folder (unless you've changed it with MultiSH4), and then it runs mostly from the data in that Save folder. You might also try deleting the Save folder - if removing the mods doesn't work - and try again. You lose your career progress and you have to re-set all of the display and sound options to your liking, but it is necessary to do quite often. Another thing you could check is to run LAA again, and make certain that it "took". Sometimes, after an install, the SH4.exe file is write-protected, and you will not get an error or warning from LAA about it failing to take...
