Hi David,
Today I've fixed it! I ended up resetting the NVRAM (after removing the JetDirect card) which then, when trying to print an internal page, made the printer display the message "Waiting for Tray 2 to pick up".
Removing the paper from tray 2 it moved on and printed from tray 3! The guys that use the printer had put a rather large stack of paper in tray 2, so I'm not sure if thats to do with it... but after resetting the paper settings its not printing fine fram tray 2 as well!
So, not sure what the problem was or what exactly the fix was, but I'm glad its working again!
Many thanks for your help and direction David :) I'm going to mark this post as the answer, only because I think the NVRAM resetting helped along with testing with the trays. But still, a big thank you to you sir!