Please try the latest firmware:
The 20161201 firmware reverts the brightness code to use software rather than hardware dimming (a feature that is clearly half-baked by the LED manufacturer, and is unsupported by the LED library I use). This should solve the glitches in those three pixels.
You can also preview the Effects mode. Open up the Particle app, select your Photon, go to the Data tab, tap “Command,” fill in the argument field with “plasma” and then hit send. Or just text the word plasma to your Game Frame if you’ve setup the Command IFTTT feature.