Hey Oink, thanks for your reply!
I'm afraid the only options when YouTube flags you video like this is to either prove you have commercial usage rights or prove that you don't need them. Seeing as I can't do either, I'm stuck with my videos being disabled for monetisation
It's a big shame because I'm sure, as the other forum post said, that Frictional Games wouldn't have a problem with it.. but there is actually no way to contact them and prove to YouTube that this is the case :/
To be honest I'm quite angry with YouTube as I've spent time playing through something, recording it editing it, and uploading it yet they flag it up and stop me earning literally a few pennies for the effort.
Thanks for you reply though, it's much appreciated!