I'm kind of at a loss, I've looked in all the places that I would expect it to look for apex source files (classes/triggers) to see if there are any files that it might not like in there but none of them are anything other than *.cls, *.trigger or *.xml.
Are there other folders that I should be checking? I have a folder that I keep in the root with a few scripts that we use but, I've changed all of those to txt files so I don't think it should be looking at them.
Any help would be greatly appreciated :)