What I could best describe as fatigue has caused me to hear bass frequencies out of tune on occasions. If I keep at it, it only gets worst.
Working with headphones will almost inevitably mess with my perception of bass after a while. And it's like one of those hidden image thingies - once I've heard it out of tune, it's all I can ear - the only cure is a break, and listening to something else for a while.
The sensation is quite weird actually, because your reference keeps drifting - almost like being dizzy or feeling seasick.