OK, so I checked all the dependencies and all OK.
So here is where it gets weird!
I've had issues with other things before where your rom names have ! in them or things in brackets like (U) and the few roms I'm using to test have that kind of naming format.
So, even though it would not explain my MAME roms not working, as they are not named like that and something as established as AM would have fixed a common issue like that long ago, I thought I would give it a try.
I editied the romlist file and took out the (U) in the name and title section. Loaded up AM and it worked, I could navigate through the menus again. Obviously this would be no good because the info in the romlist file now doesn't relate to anything.
I then removed those elements from the rom file names themselves and started from scratch. Exited AM, went back in, didn't work again!
I went back into the romlist file, put a couple of random characters in the name and title section of each line, loaded AM and it worked again.
Exited, went back in, didn't work.
I then tried adding another random character to the list but it didn't work this time.
AM discovered I was on to it and locked me out
I really am confused by this. it doesn't make any sense.