SEM and THQ - SEM Flashing gear and all lights on

[Mirthain]

I got the vertical SEM and the regular THQ and a MFH. MFH is on the THQ, I didn't get the cable with the 4 pin to USB-C cable so I decided to use the internal wire and run the SEM upside down.
Hooked them all up according to the instruction video and while the THQ is fine, the SEM isn't responding to anything, It won't accept the 3 button press to redo the settings and it's just kind of bricked. The software gives a message about an error communicating to the device, even though it recognizes it.
Is there a simple way to clear it and start over?
Also, what is the preferred placement for the MFH with a THQ and SEM. I have L/R NXT Premiums but chose to have the modules stand alone, not attached to the NXT's.
Thanks,

[fallout9]

So you have the vertical SEM installed on top of the MFH and the THQ in desktop position? Where is the GNX HID controller installed? How are the 2 modules connected to each other?

[Mirthain]

No, I've had to mount it to the left side of the THQ using the connector plate and attached using the 4 pin -> 4 pin connector. Being backwards doesn't bother me, but since it did have the 4-pin to USB-C cable, I wouldn't have been able to connect it any other way.
Sorry, got my module names mixed up. The GNX is in the THQ, THQ is connected through the 4 pin connectors internally as above.

[fallout9]

So THQ carries the GNX HID controller and it's interconnected with the SEM by the 4pin to 4pin JST cable. Also THQ is plugged to USB.
Press the Default button under Tools tab, then Find&Autoconfig in Global/External/External Devices. Make sure you're running the latest firmware and software.
If you still get an error please screenshot it and post it here.

[Mirthain]

I did run through all that, what happens is the THQ has a solid light and is fine, but the gear lights are flashing and the rest of the lights stay on. The joker screen shows both modules, but holding down the B1-2-3 buttons won't start the config cycle.
I added some I thought may be helpful, let me know if there are specific screens you want.
Also, could it be helpful to swap the GNX to the SEM and clear the ini file and try to start over?

[fallout9]

It's not only holding the 3 buttons; you have to unplug, press and hold B1B2B3, plug to USB and release the buttons.

[Mirthain]

OK, I've moved the GNX to the SEM, ran through the start up procedures along with the video. Step by step, but after the setup, every time, all the lights are on and the gear lights continue to flash. I've flashed all my devices (L/R Gladiator NXT Premiums and the GNX) to the current version. The Sticks are separate from the module boxes on their own USB cable using the GNX. Sticks work perfectly.
No change. The THQ reports back fine and the axis and buttons all test fine. Just the SEM is not wanting to set. The button test acts like the flaps/gear are set to 2 buttons, even though I set it to 3 button for both. I can see it flash across the center button while doing the test. I can't really capture it. Even when I set them both to 2 button, the flaps took the setting, but the gear still shows the bounce over.
I set the gear and flaps to axis and ran through that setup, following the video along step by step. The landing gear lights stopped flashing, but all the lights are still lit on the box and don't toggle when pressed.
The GNX light is blue with a quick red flashing. Everything reports in the software correctly, the axis all map and calibrate fine.... just seems... not right. Maybe it is and I'm just being paranoid.
Thoughts? Specific screenshots of the config you want me to show?

[fallout9]

The vertical SEM has a different button sequence for setting up the detents, are you sure you've followed the right video guide?