No com port when using hex files?

I just got a teensy 3.5 and I'm having problems understanding whether or not I'm doing something wrong or if I'm hitting a limitation. The code I'm running on my teensy is not closed source. Once I upload it with the teensy uploader tool I cannot get the teensy's com port to show up in the application that comes with this hex file. With my old 3.1 teensy this was not a problem. Is this a limitation because I dont have the actual sketch and have to load the hex file? If I load an example file from the arduino IDE then the com port shows up fine in the IDE. Once I load the custom hex then its impossible to select the com port in the custom app. I have to select a com port in the app before it can connect. Why did the old board work while the newer 3.5 doesn't?

A hex file created for Teensy 3.1 almost certainly will not work if programmed onto a 3.5. The hardware is different. The original hex file probably only work on the intended hardware.

I know the hardware is diff but I thought the first 14 pins were identical between the two boards and those are the only pins being used so I figured it would work.

The pins are the same, but each chip has numerous small differences. If you look at the source code, especially the startup code, you'll see it's filled with #ifdef checks for the various chips. Many small details have to done differently depending on which chip, even though most of the rest of the hardware is similar.

@nuggetz, just guessing here but first thought regardless of what else is happening would be that the more complex T3.5 clock setting registers will not be correctly set by a hex file intended to configure a T3.1. noting this isn't just the raw instructions per second rate but all of the subrates for the peripherals.

If you want to look deeper it would be a case of grabing the reference manuals and possibly pulling apart your hex file and a sample T3.5 one to see what is different
http://cache.freescale.com/files/32bit/doc/ref_manual/K20P64M72SF1RM.pdf
Depending on what your code does it might be possible to frankenstien a new top onto your hex file to configure everything and then have the remaining code still function (with tail wind and a following sea) but every use of on chip hardware would need checking. If all it's doing is IO port related things the low number pins do line up so those commands are probably the same at the low level.

Am not suggesting manual editing of the hex file is a useful solution to your problem, since the hours involved will almost certainly surpass rebuilding the code but if you are curious and want to learn a bit a quick look might be worth while.