Seems like the obvious difference between using the key vs. using the remote, is the immobilizer.

Do you know how your remote starter deals with the immobilizer? Normally, if you use a key without the chip in it, the starter will crank but the ECU won't let the engine start.

One way to check this is to tape one of your keys to the steering column right at the ignition switch. Then try the remote. If this works, then you know it's the immobilizer.

How long has the remote starter been in there? Does it have a warranty?