Actually, just a short while ago I discovered the culprit was a particukr hack (Advanced PM Options). I missed it for so long because it was such an unlikely hack to be causing the problems (and I had recently tested some hacks that deal with stuff like templates much more closely). I just shut down all my hacks to see what was causing it, but that's a huge job, otherwise I would've caught this sooner.
Thanks anyways for the reply