I use Gnuboy 0.6 too. It works fine for me emulating the games. The only issues I have are the flickering menu (this is gone when the game starts) and random crashes at the menu screen if i have loads of roms on my SD card. I don't know what the limit is, but i do know if you put over 500 on there, it will crash when you scroll down through them all!
As far as i know Gnuboy is your best option for .gbc games on the 2X. Describe exactly what happens and where you put your roms etc. I know that version 0.6 works on my F-100, it would be interesting to see what the problem is. If you have a F200, can someone else please say of this emu works on that?
There is a small difference between 06 and 07, but I don't think your rom problems have anything to do with it.
You need to put the roms in /roms/gameboy or in the gnuboy2x directory in /roms
You can switch between the two directories with <> in the main menu (choose select)
[edit] The flickering is solved in this version SV and I am having a F-200 so that will not be the issue.