I tested Markus' code on all my devices.
Samsung Galaxy S III (Android 4.1.1) - no flicker, but garbage lines appeared in the back over time
Philips GoGear Connect 3.2 (Android 2.3.3) - no flicker, but lots of garbage on screen
Nexus 7 (Android 4.2.2) - flickers
Toshiba 7" Thrive (Android 4.0.4) - flickers
Kindle Fire HD 7" (Android 4.0.3) - no flicker, clean and solid
iPad 2 (iOS 6.0) - no flicker
iPad 3 (iOS 6.0) - no flicker
iPod Touch (iOS 6.0) - no flicker
So, it is inconsistent behavior across Android devices.
But, if the 'EnableClearColor(0)' command is commented out, all issues disappear with all devices.
I suspect the time you might save by not letting AppGameKit clear the buffer is not worth the issues you have with odd behavior.
I should note that I did not include the SetSyncRate command in my test, I let the devices run at whatever they ran.
EDIT: Of course, the tricks you are using to fill the display by not allowing the buffer clear, that is part of your intentions, won't work without calling EnableClearColor(0). So, it is down to issues with the different devices.
Cheers,
Ancient Lady
AGK Community Tester and AppGameKit Master