There's lots of diagnostic info on electric trailer brakes in this: Dexter Axle Manual
1. Should I lose voltage after the male pigtail (the one that plugs into the truck and connect to the trailer wiring, and it is consistent down stream)?
Yes, some amount. The greater the distance from the source, the lower the voltage.
2. Should there be this kind of resistance (the magnet thing really confuses me here)?
3.2 ohms per magnet. See the Dexter manual.
3. Any suggestions on what to check and where to look?
I'd check the amperage draw at each magnet with a full 12 volts applied to the system. If you don't get about 3 amps at each magnet, you know you have a wiring problem somewhere. You could also check the amperage as it comes out of the brake controller and it should be in the near neighborhood of 12 amps (4 X 3). I found some really poor connections in how my trailer brakes were wired, especially in how trailer umbilical was attached; you could check those connections to see what you uncover. You could eliminate your brake controller as being any part of the problem by connecting a well charged 12 volt battery directly to your brake wiring and make voltage and amperage measurements. Amperage is easily measured with a 12 volt clamp on amp meter; it's a tool I often use when checking trailer wiring issues and is not too expensive. Don't leave your magnets energized longer than you need to test them, they can over heat.
Could possibly your brakes not be adjusted correctly? By the way, this should be an easy problem for your dealer to diagnose. if your dealer can't diagnose it, perhaps they also don't know how to adjust brakes.
Since your dealer can't diagnose the problem, perhaps Jayco would approve you taking your trailer to another repair facility - hopefully one that has knowledge of electric trailer brakes. It does not sound to me like your dealer is competent in the repair of brakes. Maybe you should give Jayco a call yourself. Or call Dexter. Come to think of it, when I had a brake issue Dexter was much more helpful with the warranty than Jayco.