Only remote starts if key is in ignition - Remote Starter with Keyless Entry

Often, you need to press the unlock button on the remote twice. First press unlocks the door and second press disables the immobiliser and allows the vehicle to start. The key alone will not start the vehicle.

Alternatively, when the key is in the ignition - press the remote unlock again.

The remote acts as an immobiliser device. The reason your car won't start on the key is probably because the system won't allow any key in the ignition - it is preventing theft of the vehicle. Once the unlock button on the remote is pressed the system then recognises that key is the legitimate one for the vehicle and the disables the immobiliser and allows you to start the car

The shutting off is standard procedure for the remote start if the brake is pressed without the key being in the on position. That said, it seems you may have an issue with the ignition switch. When you turn the key to the ON position, do all the warning lights on the dash come on like they are supposed to, or does it just sit there? If the lights do not come on, then you need to check out the ignition switch circuitry. The remote start bypasses all that when in use, but in order to drive the car once started, the ignition switch must function properly.

You probably have a bad ignition switch that's why the remote start will work it replicates what the ignition switch does,or you have a coded key and had a new key made and not programed the remote start module has this code stored so it can send the car the code when remote started. What year make and model is the car?

Best thing i would do is remove the battery for a few minutes and then put it back on

It sounds like the immobilizer bypass module has either lost its programming due to the dead battery or a voltage spike from jump starting/recharging the battery or it has malfunctioned. Without knowing which module is installed, it is not possible to determine if it can be reprogrammed. The immobilizer bypass module substitutes the transponder that is in your key and allows the vehicle to start. When it is malfunctioning, it may not be providing a signal or providing the wrong signal the vehicle ECU is expecting. The reason you can remote start the car with the key in the ignition is because the transponder is being read fromthe key and the ECU is allowing the vehicle to start.

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Sounds as if your immobilizer bypass is malfunctioning. To test, remote start vehicle. Check vehicle cluster (gages). If the immobilizer bypass is the issue, there will be car/lock symbol flashing rapidly. To confirm, put the key in the ignition(do not turn), remote start the vehicle. It should start. If the vehicle starts, remove key, remote start again without key. If the vehicle does not start, have the immobilizer serviced. If the vehicle does not remote start with the key in the ignition, the issue may be with the remote starter's starter output.

When you had the new keys programmed, the bypass was erased. More than likely, it was a key. Try this: put the first of the two new keys into the ignition, turn the ignition on. The theft light will light up, then go off. Immediately remove the key and put the second key into the ignition. Turn the ignition on, the theft light will come. When the theft goes out remote start the vehicle with the remote, quickly remove the key from the ignition. If the vehicle starts let it run for a few seconds and then shut the remote starter down with the brake. Wait a few seconds before testing the system.
If the above programming does not work the first time, try it again. It may take a few attempts because the process is time sensitive. You CANNOT allow too much time to pass between switching the keys.

So, this is a transponder key box, correct? And, the vehicle starts with the remote starter when you put the key in the ignition but, the vehicle will not start when you put the key in the key box, correct? If what I have explained above is the issue, there could be one of several problems. The key box may not be getting power and/or ground when running. Test to make sure. Next, the antenna ring going to the ignition cylinder may need to be adjusted to insure that the signal is being received by the vehicle. Next, if the vehicle starts with key in the ignition; also test that the remote starter works with the placed by the ignition cylinder (without being placed in the ignition). If the remote starter starts with the key IN the ignition but not with the key being placed BY the ignition cylinder, you may need to activate the key sense wire during remote start.

The PATS bypass module should have disconnected during the new key programming. First, you need two programmed keys present. Put the first key in the ignition, turn ignition on, wait for security light to go out. Remove key, immediately put second key in the ignition and turn ignition on. Wait for the security light to go out, remote start vehicle with controller, immediately remove key. Let the vehicle start and run for approximately 10 seconds. Apply brake to shutdown, wait approximately 10 seconds. Remote start to test. If vehicle does not start, repeat process.