Is the bedroom dusty or dry? (not calling you slutty just trying to help ) Could it be that he has a sort of hayfever reaction in the bedroom? Feather pillows nearby or anything like that? If you have your heating on suddely it can stir up dust from the back of the radiator and that and the dry air could be irritating him. Or it could be that he's learned how to rub his eyes and wants to fight sleep and knows that does it - in which case you're stuffed
Yeah I think new trick. Even now at 19 months my DD suddenly develops some new fidget to stop her dropping off. When she was about 9 months she just couldn't stop scratching her ears. It will go away soon I'm sure!