A few theories..Hopefully atleast one helps to solve the issue.
Please try these steps safely..
(1)In a secure area, get your rifle ready to fire (
Pending internals you may be able to dryfire) and select semi, let a cycle go. Try not to move the rifle too abruptly and select auto and let a few cycles go. If all is working properly reposition and retry(1b). (Aim in another angle)
(1a)If auto fire stops while firing, carefully move the handle towards ear and listen for any noise, while depressing and releasing trigger. If you hear a faint clicking or rubbing, the connection is fine and there is a problem in the mechbox. However, because you had mentioned that semi fire properly, I believe a problem in the mechbox would hinder this ability..So that exercise may be a waste of time but would be good to rule out.
(1b)If no noise is heard from excercise 1a, it is most likely a connection or wiring issue, either to the motor, the battery, or the triggerbox. This type of issue would create ressistance and ware out your battery prematurely, as stated by Sha Do above. You will now need to test each connection. If you find any exposed wiring please do not follow the steps below untill wiring is covered and safe to handle. Normally a current testing kit would be ideal, but most likely unavailable. You may want to open the housing for the battery and move the wires slightly while depressing the trigger in full auto. If no difference, you will then need to disasemble and check connections and wiring throughtout the mechbox, triggerbox, and down to the motor. If any problems are found, assuming you are knowledgeable in wiring and electrical currents, you already know what to do. If you are unfamiliar please do not proceed and seek assisstance as this could be dangerous because of possible electrical discharge.
If no problems are found in wiring or connections, there are a few other ideas..
(2)Power- you may have a battery that has insufficient power. Either because of long term use/abuse or it just isn't the proper battery. Try a newer battery of equal power, or a newer one of greater power and test the performance.
(3)Motor may also be on its last legs and either due to long life or prior wear and tear or abuse may need to be replaced or repaired.
I've lost my train of thought...Hopefully what I've provided is helpful. I apologize for the lenghty explaination, but it is a difficult problem. I've had identical one with 100% of my older armalites. If you're unfamiliar with these methods I would be happy to do the work for you. Just contact me for details, or one of the many gundocs on the sticky thread "Calling all gun docs" you should be able to find one in your area.