I have a AFS 5500, Gtn650, Vizion AP, and a Gemini PFD.
First, I would ask both AFS and Trutrak if they have specific sample schematics for the Gemini AP. My assumption from taking a quick look at the Gemini AP manual is that you would wire it just like you would a Vizion or AFS Pilot. Those sample schematics used to be on The AFS website. If they arenít on the new dynon site, I can email it to you.
The ARINC in/ out and one rs232 circuit from the 530 goes direct to the 5600. Then the Gemini is wired to the 5600via Arinc and a Rs232. Then the AP is controlled from the AP button on the 5600.
If you want to email the schematic you wired your panel, Iíd be more than happy to review it.
It sounds like Arinc data isnít getting to the EFIS, which in turn isnít getting to the AP. It could be due to a bad installation (wrong pins wired), an open circuit, or an Arinc module not working.