raparici, I've been updating my post as I find new information that may be helpful to your issue. Maybe you missed this in my post. I think it may be worth a try.
2600-daptor II stripped FB1.hex - try this if you want to use with emulators other than Stella & EMU7800. This gets rid of the z-axis and disables button 1 when in 7800 mode - these can confuse the controller mapping in other emulators.