You probably still have a leak somewhere. The controller closes the control solenoid and gives a shot of air from the supply solenoid on the PCU to open the dump and wheel valves to the PCU. Then it looks for a stable pressure reading on the pressure sensor on the PCU. If that reading is not stable, it faults and starts flashing lights and opens the control solenoid to depressurize the system. Unfortunately this process is fairly brief so finding leaks with the controller running the show will be tedious.
A better way to search for CTIS leaks is to disconnect the cannon plug from the controller and jumper the control solenoid pin to the 28V pin in the connector. Then briefly jumper the supply solenoid pin to 28V to give a shot of air to open the dump and wheel valves back to the manifold. Once pressurized and the control solenoid energized to hold that pressure in the system, you have all the time you want to go over all the plumbing with bubble mix. Having the system fed with a compressor will really help as you can hear things better. Having my PCU under manual control made finding my system leaks pretty easy. The CTIS controller will err on the side of caution, so it doesn't take much of a leak to fault the system. I have pics of the connector with the necessary pins marked to do this, that I can put up later if you want them...