I read through your posts in the other thread, but I have no idea how to help you. In my case, getting the ipac2 to work with 6.0 was just a matter of creating the correct dummy file and remapping the P1 controller in RecalBox, using the standard procedure inside EmulationStation (pressing a button to detect, then filling the remap table). Not much to describe here.
For the record, I also own a DualStrike v3 single player encoder, from ArcadeForge, and it also works fine with Recalbox, using the same X-Arcade "driver".
I remember having some problems with "disappearing" buttons, but these were due to bad wiring/soldering/terminal contacts near the iPac2. After checking my wires, I retested the encoder in Windows, using a proper keyboard tester utility, and made myself sure the encoder, wiring, P1/P2 buttons and sticks really worked as intended.
Once hardware problems are totally sorted out, if you still have your encoder detected as keyboard, then the dummy file may be incorrect. In my case, I had two options for the filename, but only one worked - see the mini HowTo for details.
If this still does not work, the only conclusion is that we have a encoder incompatibility with Recalbox... that would be really bad luck