The website has pictures that explain how to use precision X1.
 
https://www.evga.com/precisionx1/
 
Try changing settings.

I just went through the firmware update for my 3090.  So did all 4 red LEDs come on and the fans were spun up during the firmware upgrade?  Since you say it completed, there must have been the progress bar..
 
If it were a problem with the firmware upgrade, I wonder if there is a way to re-do that process using the same version of the firmware?  Precision X1 seems to work OK on my system, but having some problems with some settings..

DeadMedic
In my experience there are some settings that are persistent after P1X set's them. I was able to set the led on my 2080 ti hybrid, uninstall P1X then use Afterburner. The LED setting stayed with LED Sync. My advice would be the following:
1. Uninstall P1X
2. Uninstall LED Sync
3. Reinstall Driver
4. Reinstall P1X & see if you can change or fix anything.
Lastly you may try a BIOS flash if EVGA can supply you with one.

Tried all that, didn't change anything.  Spoke with EVGA tech support.  They also recommended flashing the bios.  Although strangely, he said I *had* to flash it to the beta bios listed in the pinned thread here on the forums instead of simply re-flashing the most up-to-date non-beta bios because "The US EVGA office doesn't have access to the stock bios, and to get it we'd have to contact the Taiwan office and wait a week to hear from them."  That made absoultely zero sense to me.  Why in the world wouldn't the US EVGA team have access to the stock bios?  Either I don't understand how this kind of thing works, or the person I spoke with was mistaken.

Anyway, I flashed the bios to the beta version, but it didn't work.  RGB bar is still nonfunctional, no RGB control button shows up in X1, and the third fan won't turn on.  He said I'd probably need to RMA it, which I am in the process of doing.  Really disappointing to wait a over a month to get a card and then have it turn out to be a lemon.

Saltgrass
I just went through the firmware update for my 3090.  So did all 4 red LEDs come on and the fans were spun up during the firmware upgrade?  Since you say it completed, there must have been the progress bar..
 
If it were a problem with the firmware upgrade, I wonder if there is a way to re-do that process using the same version of the firmware?  Precision X1 seems to work OK on my system, but having some problems with some settings..

Saltgrass
I just went through the firmware update for my 3090.  So did all 4 red LEDs come on and the fans were spun up during the firmware upgrade?  Since you say it completed, there must have been the progress bar..
 
If it were a problem with the firmware upgrade, I wonder if there is a way to re-do that process using the same version of the firmware?  Precision X1 seems to work OK on my system, but having some problems with some settings..

Yes, four red led's near the power cables turned on, and all three fans ramped up during the firmware update.

Oof, that sucks. Sorry about that, hope you can get a replacement without too much delay.

Had this same behavior after I flashed the OC switch 450W bios. Turned my PC off, switched it back to Normal mode and it behaves normally, with the LED button reappearing.
 
The all red power LEDs and fans to 100% during flashing is normal behavior.
 
I would highly recommend, uninstall PX1, turn your PC off, switch to normal mode on the switch, reinstall latest PX1 ver 1.1.0.11. If LED button comes back, then turn off PC, switch back to OC mode, and check if your LED button reappears. This is what I had to do, now all is well.

Contact support & see if you can get them to give you the older firmware to flash it back.

SeanDude05
Had this same behavior after I flashed the OC switch 450W bios. Turned my PC off, switched it back to Normal mode and it behaves normally, with the LED button reappearing.
 
The all red power LEDs and fans to 100% during flashing is normal behavior.
 
I would highly recommend, uninstall PX1, turn your PC off, switch to normal mode on the switch, reinstall latest PX1 ver 1.1.0.11. If LED button comes back, then turn off PC, switch back to OC mode, and check if your LED button reappears. This is what I had to do, now all is well.

Thanks for the response.  Yeah I uninstalled the software, reinstalled the driver, and tried both bias’s available with the bios switch, including flashing both.  None of it worked.  Tech support said I’d need to RMA it, which I am in the process of doing.

Yes. I experienced this with a 3090 and a PX1 FW push as well. I requested the shipping bios and FW from EVGA but they aggressively denied the request over the phone...

Wait, so PX1 forces you to update the firmware? That's not cool.