So I think I found the issue, I checked my “good” clock PCB and the crystal has roughly 0.8V across pins 1 and 3, however, my RGB sign board has 0, along with the pins tied to the MCU. When looking at the layout, I placed a long 3.3V trace on the front copper of the PCB. This is NOT good practice, and I feel is causing some sort of issue. Either way, I know now it’s 100% the crystal causing the problem. Not sure how to fix something like this though without ordering a new board…
MAYBE you have the 4 pin crystal package 90 deg misplaced ???
nothing wrong with your 3.3V rail like that. BTW, that has nothing to do with it.
Doesn’t seem like it, I verified the 4-pin crystal package several times, and figured that there shouldn’t be traces running underneath. What can cause 0V at the crystal?
Is this an active crystal oscillator that produces a ready-to-use square wave? IIRC one of the pins is an enable pin and grounding it disables the oscillator. I see you have two pins going to GND.
A fraction of pF extra capacitance due to a track running underneath will have no effect on an active oscillator where the circuitry is inside the can.
Rotated 90 deg / That’s my bet, anyway, I have seen it done before… what happens if you put an ohm meter across the MCU pins with the board not powered ?
I don’t remember - have you write or not if at IC (crystal) pins you also have 0V?
0 ohm resistance across all MCU pins that I checked regarding the crystal traces and ICSP header
Yeah at the crystal pins is 0V, but I did something stupid and tried to see if I could power it externally with a power supply at 0.8V, the supply started drawing 600mA of current and now I probably fried the MCU and crystal. The MCU still has 3.3V at the test point I measured at and nothing got hot, but something is pulling down the crystal and I really don’t know what.
Such experiments should be done with 1k or more in serie with voltage source.
Or not done until you have a theory of what you did wrong, then test to prove/disprove if you can’t prove/disprove visually.
At least you know what is wrong now . . . time for a new board if this one can’t be salvaged, but figure out why it didn’t work first.
That’s my problem, I’m struggling to find what caused the issue.
Yup, that’s what Engineering is . . . the struggle to find a solution to a problem, if it were easy everyone would be doing it 
Just keep at the front of your mind that there is indeed an answer that can be found . . . and no amounts of crossing fingers or touching wood makes any difference.
My old design doesn’t even make sense in principal that it works, assuming v stray is 2pF and the crystal on digikey says CL is 9pf 2(9-2) is 14pF for each cap on the crystal line yet that doesn’t seem to be the case. I can upload and boot load code every time without fail on that design. Luckily I ordered an extra crystal so I’ll try and see if I can change it out.
I still bet the crystal is 90deg, and the output pin of the oscillator is may be shorted somewhere…
or the micro is not in square ?
The micro was placed on by a machine by JLC, and the crystal is placed upside down along with the MCU as its on the back copper of the board, looking at the datasheet of the TSX-3225 it says pin 2 is ground which is where I have it.
Oh! Come on mods this is going on long enough.
This is not a quick ‘brain fart’ minds gone blank question like we alm have from time to time - the OP is continuing to ask about a howto concerning electronic design!
So you have a bit of progress and thats awesome 
and what @RaptorUK said was spot on !
I think you can stop worrying about the load caps and stuff and I too would be surprised if you 3v3 had anything to do with it so go over connections check orientations check for shorts etc. Good luck with it.
The 0.8V on the 3,3V rail is not so silly
You can use this with a thermal camera to see where the current is going.
Beware,
There seems to be a short between the two crystal pins, no matter how much solder I remove there’s always a short, which means I damaged my second board. As for the first one, no short is there, although I initially installed the ICSP header in the wrong way when trying to bootload.
Not sure if I should try and assemble another board or just order a new one entirely, as I’ve revised some of the layout.
Remove the crystal and measure it again. It’s only a few short tracks, and it should not be hard to find the short. Ceramic capacitors can also fail in a short circuit way. There is a possibility that the short is under the microcontroller. In that case you would have to look under the uC itself. At the very least you can get some soldering practice out of it 
Another option is a fault in the pin configuration, or a faulty uC itself.
Finding the fault is also not only for getting your project to work, but learning how and why it failed is also educational and can help with preventing making the same mistake in the future.