As touched upon in one of my earlier posts, I was intending to use "ken rename" to bulk rename the game files and the associated image files, then do a "search & replace" in the xml file to refer to the new file names.
Thankfully, nexusone13 tested my files and had the exact same problems as myself, and renamed the files for me, removing the 3 spaces in each file name.
This seems to have done the trick - it looks as if it was the spaces causing the issue and not the "STE" in the filenames.
To be honest, I wasnt sure it would be the STE causing the issue, as there are games out there that have those letters in the file with no problems (eg any game with the word "step" in the title).
Anyway, with the 3 spaces removed, I have booted up the ST emulator, played games, reset the Pi, shut it down, did a quick shut down as well, put the usb stick in my PC and booted up ARRM, and........everything now seems fine !
Thanks for all the help (especially nexusone13), and suggestions everyone.