I too am experiencing the Canvas flickering in GearVR builds. Flickering occurs in the right eye only when the canvas updates, in my case I am enabling / disabling an image component on mouseover, using gaze tracking as well. The canvas contains a scrollrect, and a large number of image and text components that overlap. Haven't tried with 5.3.1p2 yet, I'll see if updating fixes it, and if I can reproduce it in a simple project.
Great to hear that someone else is having problems, too ;p. I spent a fair amount of time trying and failing to reproduce it in a minimal project. If you manage it, please pass it on to Will at Unity.
Scorched Battalion - VR Jam edition available for Gear VR and DK2 (Win/Mac/Linux) Jungle Juice Sven Co-op