It kind of sounds like the Usage Profile under the door template that you used.  You can specify how the LED operates under different circumstances (Grant Access, Deny Access, Mode open, etc).

Try editing the door with the reader you are having problems with, select the "Usage Profile" menu item, then check the values that show up to the right.  If they all say "Solid Red" you can change them there.

If that doesn't look like the problem then perhaps the wiring for the status LED on the reader is incorrect.

Good luck.

I have seen the LED control circuit on gateways and reader modules get damaged when the reader is hot plugged onto the gateway or reader module.  If you measure the voltage between pins 9 and 5 on the reader connection (reader 1 or single 10 wire) you should see 0 volts when the LED is green, and 5 volts when the LED is red.  For the second reader it would be between pins 9 and 4.  If the profile is setup correctly, but the module is not putting the right voltage on the noted pins, then the module would need to be replaced in order to get the LED working again.

Hope this helps,

Mike