I have seen a 990 base fail with very strange symptoms. I had my TMCC command viewer software active so I observed illogical commands being transmitted by the base out it's serial port and LCS WiFi. What was broadcast to the track is unknown but if it was the same bogus commands as transmitted out the serial port, then it would account for loco failures. Several engines would not start or run, others seemed OK. I replaced the base and all was good again. Firmware/memory/hardware failure is suspected.
Since you have engines that start in conventional, I would suspect the signal output from the base. If you have a TMCC1 base, unhook the 990 and try the TMCC1 base's output to the track. If the loco still won't run under TMCC1 command, then follow GRJ's advice and re-seat the receiver board.
Dale Manquen's archives describe how to test the 990 signal strength with a multimeter. I found that test to be of value when verifying poor signal strength on large layouts. A good signal strength (i.e. voltage), however, does not ensure that good information is being broadcast from the base. If your locos run with a different base, then send the 990 back to Lionel.