I can't help you on the flickering problem. I can tell you that all their libraries are compiled and closed source, so no porting the Mikro Gui's. Maybe ST has an open source library? I know with pic micros, Mikro repackages the Microchip GUI libraries as their own.
I contacted their tech support and the flickering seems to be a hardware issue. They don't have a solution for it. The battery charger is also buggy. It usually won't charge the battery fully and sometimes not at all without power cycling it multiple times. I'll probably go with keil MDK-ARM professional which includes their RTX rtos and emwin gui library (and gui editor program for windows). I've used RTX before and it's small and efficient, but has a limited feature set. Keil also includes libraries for a flash file system, tcp/ip, and usb drivers (including mass storage).
ST is offering a free version of emwin for their cortex processors, but omits the gui editor
I'm trying to figure out an easy way to do firmware updates, either through the USB or by swapping SD cards.