Idk if this is helping anyone, but by me the sim card problem appears on every rom, BUT when the popup appears and I reboot my phone (sometimes the popup come back after the reboot and I have to reboot again) But then the sim card error doesn't appear again, so long I not restart my phone or shut it down.
I am sure you have already checked this - but just in case,
there was one time when I was placing the battery cover back on the phone where I must have somehow touched the sim card in the process and it was not sitting correctly in the sim card holder. I was getting random sim car errors, depending on the angle of the phone, etc. I reflashed a few different roms, flashed back to stock, etc but still had the random errors / messages.
By chance, pulled the cover off again and noticed the sim card was loose. Clicked it back in place and have not had a problem since.
As noted, you have probably already checked this - but sometimes the simple solutions are overlooked
Good luck,