MarkTheCaz:
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).
Yun 5V give ~4.5V is hardware bug. Someone at this board post hardware mod by short diode but it will be void the warranty. What is your RFID reader's model? for testing purpose you could separately power up reader, and only connect ground, Rx, Tx between reader and Yun.