I think either its a problem with your PSU or most probably your PSU is overloaded or in rare situations it may be a malfunction of slef monitoring. Try to check it with one of your friends PSU which has same wattage as your current one. If still your readings are low try some higher rated PSU. If problem is still their, just ignore it.
Mines isn't doing a great job either. 3.15V for the 3.3V rails, read from Everest. Oh well, the system is doing alright, so I should be worried. But if I buy a new VGA, I would replace it anyway.