Very weird behaviour on D33 on Teensy 3.2

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TnF

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So, i am working on a custom keyboard project and i have finally a fully working prototype on my custom pcb. I'm using a Teensy 3.2 soldered like this so that you solder it directly to the board and all pins are available.

v6JkcxH.jpg


The reason i used this side is so that the led and reset switch are accessible.

D32 and D33 are connected directly to a rotary encoder for the 2 channels as well as ground.

When i tested it separately it was working fine. However now that is connected to the board it causes the Teensy to crash and disconnect and the encoder works very choppily.
I checked for shorts but can't find anything, and i don't have a desoldering pump to take it out from the board and check the underside.
The only misconnection i had was 5V (from USB) directly to A11. Teensy was getting warm (not hot but enough to be noticeable by feel) and it took me a long time to find the cause of the issue (it was a mistake in my drawing schematic)

Now if i run a blink program to D33 it causes it to crash and reboot indefinitely even after i remove its connection to the encoder! I even tried pulling it up with a 10k resistor but same issue.
I bodged a repair by using D13 in place of D33 after i removed the led resistor and everything works fine (it was the only spare digital pin i have).
In order to find out the cause of the issue i either need to desolder it from the board and check, it or solder a new board with my spare teensy with header cables to see if i can reproduce the issue.

My question is that since D33 is finicky and should not be pulled to ground maybe could be some flux residue (even though i've cleaned it with alcohol) that is causing the issue or could be even damage from the 5V on A11?

Kind regards
 
In the past, pin D33 was special. Here is a quote from Paul from the 3.1 time frame:

Pin 33 on the Teensy 3.0/3.1 is special. It defaults to a non-maskable interrupt (active low) with a pullup resistor. When it's low on reset the MCU enters EZ Port mode, which basically turns the MK20 into a SPI flash chip. If you weren't using Teensyduino this might be how you'd upload a new program.​

In theory the new bootloader chip (MK02/04) fixes the problem in Teensy 3.2.
 
In the past, pin D33 was special. Here is a quote from Paul from the 3.1 time frame:

Pin 33 on the Teensy 3.0/3.1 is special. It defaults to a non-maskable interrupt (active low) with a pullup resistor. When it's low on reset the MCU enters EZ Port mode, which basically turns the MK20 into a SPI flash chip. If you weren't using Teensyduino this might be how you'd upload a new program.​

In theory the new bootloader chip (MK02/04) fixes the problem in Teensy 3.2.

I'm aware of this, however i'm not sure what might be causing it to behave like this. It could be a short to somewhere, but where? Nearby pins seem fine and it is the only pin having trouble :/
 
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