When I removed this option the miner took 10 minutes or so to fully spin up but when it did it finally reached full hashrate on the pool that it wasn't hashing well on.
You kind of answered the mystery by yourself, it's the "fast boot" that makes a difference, not the pool, the pool part was just a coincidence.
the fast boot will speed up the upfreq which you see on your miner's status page, all 3 boards will start with upfreq 0 and when all are tuned to their best ability they will turn to 1, the default tuning is a bit slow, so they introduced this fast boot to make it tune faster, however, as a result of this "fast" boot, some of the boards might not reach their maximum frequency and thus the miner will hash at a lower rate.
Keep in mind that even if tuned fine for one time, it could be bad in the other, it could be bad when you first test it, then on the second time it would be good, so my guess is you had pool x with fast boost enabled, the tunning was bad, you changed pool, the tunning went fine this time, so you assumed it has to do with the pool, if you kept the "bad" pool and rebooted a few times, you would eventually get it to hash at full speed.
It's great that you brought up that fast boot to the discussion, I advise AGAINST it unless you have these two things:
1- your farm encounters many power outages and you want your miners to tune in as fast as possible.
2- you have some monitoring software like AwsomeMiner which will automatically reboot the miner in case the tune doesn't get to full hashrate.
If you don't have the first one, there is exactly no need for fast boot, if your miner reboots once a month, why risk having a bad tune just to save a few mins? if you don't have the second one, what happens if the miner tunes at 70% of the hashrate and you don't notice it? it would be better to let it take its time to tune at 100%.
Alternatively, if you do care about fast tuning, you could use the upfreq speed option in the tools, it has a scale from 1 to 10, the higher the number the faster the tunning but the more likely the issues, so you could test something in between, maybe 4-6, then do a few reboots to make sure your miner tunes fine with every reboot and stick to that number.