We had the exact same issue when we upgraded to 6.1.3.4 from 6.1.3.1.
We had our ap on the local lan have difficulty upgrading but they finally got their load. Our remote office in NY none of the aps upgraded even though the controller showed they had upgraded and up and running. When we came on monday some of the APs showed they were up in NY and other showed they were down.
the latency to our NY office was less than 80 ms and the ap in NY were stuck. We ended up haveing to clear the os at least onece and some cases 2-3 times and then force a reboot from the cotroller before they would come on line.
There is a open TAC case we have which they are looking into I would recomed you do the same. I think we have documented a few bugs in the .4 code release.
you are not alone.