Did You try to clean all the configuration files within failsafe mode or using the -n flag with sysupgrade? (beware: this will remove all files and installed packages from the omega).
I've had a similar issue, when I didn't deliver enough power to my Omega2+. After I've attached two 47 µF capacitors in parallel to the 3.3V rail the issue disappeared, but I wasn't using a proper extension board! This probably isn't related to Your issue after all :)