I have the exact same machine and you are doing what I used to do. Trusting that when you do a sheet cut it is dead-nuts square to the rest of the roll. Then lining that "square" edge up to the separation lines in the platen. Wrong wrong wrong! And heat has nothing to do with it.
I have a new loading procedure that goes by feel instead of visible cues.
Works a treat. We just printed a 79" double sided banner using this method. It was out only 3/32".
When you load you media you need to reach under the machine and put one hand on the roll of vinyl, banner, whatever. Then grab the middle of the media with your other hand and pull taut. Then slowly move the media side to side. You will feel the "center point". Once you are on center drop the wheels.
I learned this after a huge batch of decals got wrecked. I noticed the cuts were progressively worse so I started with the basics. Got out my precision T-square and found the roll was nearly 5/8" out of square. Holy smokes!!! I asked the wife how she was loading, cutting etc... She said she would run a batch of a hundred, sheet cut, repeat. It was a matter of stacking tolerances and trusting the machine to be accurate when feeding. they are not. Look at the tracking specs for any of the printers. not that great.
The only way you are going to get truly perfect tracking is on a roll to roll set-up with a nip point and most importantly a web-guide. I know this because I built and qualified such equipment for over two decades.
Best advice is to re-zero every 6 to 10 feet of material. You will have smooth sailing.