1. Either there is a bent pin in the OBDII port or a pin has gotten pushed back out of the connector. It happens.
2. Romraider cannot delete codes from the DTC section on the 16 bit ECU. Disabling from here just stops the CEL from coming on with the DTC. The DTC is still active though. You physically have to go into the hex file and change values. The DTC "fixes" in the OBDII section are just that.