So noticed that the Pebble Android app drain started again last night when I was going to bed. I promptly clear my Dalvik Cache and Cache partition and the problem went away, based on my last battery check. The only change to my phone was installation of couple new watch apps.
Still need to test out, but is it possible that installing the watch app might corrupt the Dalvik Cache or put Pebble in a bad state, where it keeps waking up the android phone?
I am going to run few test by uninstall some watch app and see if Pebble Android App start waking up the phoen from deep sleep. If not, i'll reinstall couple apps back and see.