Same for me in Thomas' War. No problems at startup, seems like game starts normally, but eventually it loads only the map but no interface of any kind. No error messages at all!!!
I have BtS 3.19 and Win XP. I know this mod leaves the dlls, so it is unlikely to happen because of the civ upgrade. And if i remember correctly it was the same problem when i had 3.17, altough I did not try with that version today just months ago...
So I'm pretty sure the problem doesn't connect with the version of my civ 4, but i have no idea how/where to find the bug
EDIT: found out that this is/was many other players problem too, so i don't expect any quick solutions. Just hope something based on tsentom1's first post might work eventually...