I'm not sure what emulator the Gamestation runs, so it's somewhat hard to figure out what might be wrong. If you could figure out what it uses that would be great. Seems the hardware landscape gets worse for homebrew devs as we now have to take into account all this oddball hardware.
I mostly used Stella and a mouse when developing, and the light four-switch "Darth Vader" plus the 2600jr for real hardware testing. Not sure what the Flashback 2 uses for hardware, maybe some form of reimplemented TIA + 6507? If it's FPGA based then maybe there's a firmware upgrade. Other games using 12-digit displays, especially with early HMOVE, might also be good test beds. Demos too.
Seems to me the best way to play 2600 games is still the original hardware + flash, or a regular computer running Stella with suitable USB controllers. Atari actually seems to make a decent wireless joystick+paddle combination controller that works with Stella. There are some other paddle controllers on the market as well - no need to give Atari any money.