Hi!
Don't be worried, your FXPakPro is working great: the "SNES Sprites" feature of the SGB does flicker, whether you play it on real hardware or emulator. I designed the game with a plain white background to try to mitigate this issue, but the SNES sprites will still appears translucent / ghostly due to the constant flickering.
I'm sorry if the game page description wasn't clear on this topic, but this feature is flawed due to the flickering, and that's likely why Nintendo disabled it. The "fix" performed by this game is to be able to enable this feature back (it's normally locked away), but I don't think anything can be done to prevent the flickering.
I tested my SD2SNES (previous name of FXPakPro) and it does emulate the SGB1 and SGB2 perfectly to my eyes: I didn't notice any difference running my through an actual SGB / SGB 2 and the FXPakPro while testing my game.