I put the mag mount on top of the car and ran it through the door. Doesn’t look like the coax is getting pinched.
OK, that's good. Just be aware of abrasion and water intrusion.
The weird thing is in some areas the antenna just won’t work. For example I just went to the grocery store with the antenna and I had no trunking signal with the antenna in the parking lot. I unscrewed the mag mount coax bnc from my scanner and put in the rubber duck and I was getting reception!! How is it that I was getting signal with my rubber duck and not my mag mount antenna!!?? What’s wrong here?
Could be a number of things...
With some scanners, a strong nearby signal from a cell tower or other transmitter can over power the receiver (even though it's on a different frequency) and effectively deafen the receiver. Think of it as being at a party and trying to listen to a cute girl with a soft voice, meantime the drunk quarterback is screaming in your other ear.
Simulcast systems can have issue, too. The signals arriving at your antenna at different times can effectively cancel each other out. Some scanners are not good at handling this.
Could be an issue with the antenna, mount or connectors.
And while the exterior antenna should work well, the disguise antennas are not your best choice. They are a compromise between performance and looks.