You should have rebooted - without a reboot, InCD probably wasn't disabled properly.
For now, it sounds as if your drive is stuck with incomplete firmware, in some kind of 'default' mode. A misflashed 2500A identifies itself as a 2100A with a 0.0something version and the LED doing odd things - this sounds very similar. The way out of this is probably to turn the computer off, then boot with a DOS floppy, and use a DOS flashing tool with a .bin firmware.
Whilst I've no direct experience on this drive, it looks as if you can get what you need (other than the boot floppy, which you'll have to get for yourself from elsewhere - in many versions of Windows you can make one using the floppy disk formatting program) from herrie's 1300A download page. "NEC 1.0A RPC 2 (Normal) DOS" should be the official 1.0A NEC firmware with DVD region protection as standard.
Before attempting a DOS reflash, I'd be inclined to seek advice from those that know (possibly by reading herrie's forum) as to whether it's worth getting the stuck disc out of the drive using the emergency eject hole (you are supposed to flash the drives with no disc inside - but you may make things worse if you flash with the tray sticking out of the drive) and whether or not you should remove any other drives from the same cable when fixing this misflash.
At least the drive is still being recognised by the computer - so it should be fixable. It's far harder to get a drive back if it's no longer recognised by the computer at all.
If you flash the drive successfully in DOS mode, once you get the DOS prompt back, turn off the computer, wait ten seconds and turn it back on. You need to power-cycle the DVD writer to start its new firmware.
(who is offering what he believes to be valid advice, but can take no responsibility if this goes wrong and you permanently 'brick' your drive)