Thanks for the above replies, still banging my head against the wall a little.
I'm not sure the differences between the Uno and the Leonardo/Yun are the issue here. I've got the RFID working but it does so intermittently.
Yesterday it was fine, today it's not. The only thing I've noticed is that the 5v coming out of the yun is not 5v: when the rfid works it's about 4.5v, when it's not working it goes down to about 3.7v. Dont know why this might be (or even if it is worryingly low: my instinct says yes).
I'm guessing something is shorting out or drawing too much power(?) I've had a search on the forum but cant see anyone else having this issue, is it likely to be the problem? currently I get 3.8v, if I remove the power lines to my breadboard I'm getting 4.0v. Dont know if this is even the cause of the problem, but I'm not sure what to try now: I'd be happy if the board worked all the time, or have something to work with if it failed all the time but this sort of situation (with a tight deadline looming) is pretty stressful.