After reading other posts with similar issues to kinda of get an idea of what was going on, I did some more fiddling. What I currently THINK is going on in my car is that when I put the key in and turn it to start, the key passes through 'ACC', through, 'ON' and finally to 'START'. So basically the unit gets power starting when the key is in ACC, which is a few milliseconds before the starter cranks. With most remote starts, this gap is much longer, as the remote start energizes things one by one - including any key bypass modules etc.
Anyways, what I think is going on is that the unit does not like the power drop when it is already on, even if its only been on for half a second. I dont think it requires much constant power to retain memory when it is off, but I think when it is booting up and experiences a voltage drop, weird stuff starts happening.
**Other posts suggest using a combination of a small rechargeable battery, battery charger, diode, and relay(s) and the idea would be that this setup would supplement the incoming voltage for the few seconds it drops during starter cranking. A capacitor in place of the battery would simplify things but there are arguments against that as well. Another advantage to this is that if you were hanging out in your car (car off) listening to music, then started the car, the stereo would be on the whole time. So you could stop for gas, turn the key to ACC, pump your gas, and restart the car without restarting the stereo.
**A simpler idea is to use a timer relay, such as the DEI 528T. Its around $20-30 and the idea is that you can use it to delay the stereo from turning on (until the engine is done cranking). The timer would basically start once it was energized by turning the key. The downside is that 1) for it to help with your extended remote start times you would have to increase the timer setting on the timer relay, and it would make your startup times when you use the key noticeably longer (sucks bc its already long).
**A third option for remote start induced problems would be similar to a timer relay, but to use on of the AUX outputs on your remote starter to control a relay. Most alarm systems can be programmed to turn the AUX output on with start etc. This would only work if you could program it to come on after the cranking. A cool plus side would be that you could turn your stereo on and off with your key fob.
**One last option is just something I came up with in my head, dont know if what im thinking of exists. What would be convenient would be if there was some kind of relay in which you could set the 'trip' voltage. In other words, maybe something that interrupts the circuit if incoming voltage drops below 10.5V, thus giving you only 0V or 12V and eliminating the situation where the stereo gets under powered and acts screwy
These are just my ideas, Im not positive on the problem or the solutions, so if anyone has anything to add, please do!