Qdeathstar:
I have the transformer plugged into a power conditioner.
What transformer ?, you have not mentioned this before.
sorry, used transformer/psu interchangeably. I have it mains >> conditioner >> psu
Qdeathstar:
I know it's not recommended but if I cut the ground lead off the transformer would that do anything to isolate the ground?
If you have a TN-C electrical supply then earth and neutral are connected together anyway.
Lot of power in that flash, changing something could blow your strip.
Only solution i can think of is to use a CTE isolating transformer and derive a local earth.
For a test though you could try a battery and only illuminate a few pixels.
Dont forget to isolate the arduino as well.
Looking around i see that some of those supplies can be made to float by cutting links inside, i dont know your abilities though , those supplies can be lethal.
Ground and neutral are tied together at the panel by two ground rods and cold water pipe.
I head you mention an isolation transformer earlier... Something like this to try?
Also,I'm going to run it at full brightness today and see if I still get the blink, as I hadn't done that yet I just realized.
Possibly.
Need to know what type to sort out the earths.
My technical mains uses the CT type.
Qdeathstar:
Ground and neutral are tied together at the panel by two ground rods and cold water pipe.
Cold water pipe is just to keep everything at the same potential for safety.
Unless your incoming water main is metal it improves nothing.
The presence of the two ground rods makes me think this is a rural rather than urban setting.
Possibly with overhead supply lines.
Can you say your geography. ?
Qdeathstar:
Mark the strips are ran inside of aluminum Chanel that is glued with double sided 3m tape to metal flashing.
These strips can be used on roofs apparently , the architectural suppliers do exactly that.
Channel is of course earthed
Maybe I need to earth my channels, as they are not currently.
In the United States NEC code requires at least be ground rod (local requires two) and requires cold water ground. My pipes go into the earth as metal.
I have overhead lines at 120/240 but those are atleast 40ft away from my lights, and there are no transmission lines for atleast 100ft, those are probably 11kv (but I'm not sure)
My nuetral has zero potential to earth ground. I am certain of that.
As a kid i had a party telephone that used to occasionally go ding.
I discovered that nipping outside and having a wizz on the earth electrode solved the problem.
Maybe a hosepipe would help ?
hmm. well, I would try pissing on it, but as its mounted upside down splashback is a real concern... what type of goggle do you recommend for this type of work?
Qdeathstar:
, but as its mounted upside down
Well there is your problem, its not an earth electrode, its a lightning conductor. 
Turns out the simplest solution was to slow the refresh rate down. I was unaware that FastLED had an option to slow the refresh speed to below 1mhz. I have slowed it down to 1khz and now it blinks maybe once every two days, but only at the last 20 or so pixels. I'm going to try to add a timer to only refresh the less once every 2 milliseconds. That should get me down to 500hz. I think that will completely solve the problem.
Thanks for all the advice though. This is a solution, but maybe not the solution. 
Glad you found an answer that worked .
Maybe your origional idea of the signal lines was the problem.
Qdeathstar:
to slow the refresh speed to below 1mhz. I have slowed it down to 1khz and now it blinks maybe once every
Missed that i think the max speed for neopixels is 800 KHz
Yeah, neopixels are ws2812. Ws2801 is good for 4mhz, but that requires an almost perfect environment. In most environments it's 2mhz, and on a run like this which is actually out of spec (finding that out now) it needs to be turned way way down.