Hello, same problem as you with latest update of Xperia Z3. It seems to be related to Marshmallow.
An other topic talking about it:
By my side, I tried a lot of things, including factory reset of the phone.. without luck.
So, I rollbacked to lollipop on my phone, and the problem disappeared. I won't update to marshmallow again until the problem is not solved.
I hope that pebble will found a workaround.. I'm afraid that sony won't fix this mess, since they said that Xperia Z3 won't receive Android N update.