There could be any number of problems with the power supply. It sounds like the problem isn't causing any service interruption yet, but I would put a call into JTAC and futher troubleshoot the issue and RMA the power supply if necessary.
I just had a problem with an EX4200-48PX stack of two switches. They too were reporting PEMs not supported and my Cisco 1240 wireless access point didn't run off of POE. It seems that the newer PX series of EX switches must have the new PWR2 power supplies. Once I inserted the PWR2 PSs everything worked.
