New here but I have some possibilities:
First have to say you definitely can't do this without an interlock!
Taking the your statement at face value - that all breakers are off (and not defective) suggests one possible scenario: The generator could have a miss-wired cord/socket, or plug. If the neutral is switched with a hot pole, it would feed the system ground with 120V (through the bonding or ground rod systems).
Although this would not explain the breaker tripping in the main panel.
I think here should be a ground rod for the pool.
If the resistance of the grounding system(s) is less than 4Ω, and you have a wiring fault, it would draw more than 30A. I am wondering if the breakers tripped immediately when the neutrals were tied, and tripped slow and loaded the generator when you isolated the generator neutral?
Check all your plugs and sockets' wiring for proper wiring. Try volt checks to confirm they are right; THEN, try and see if there are any sneak loads you missed...
Bottom line is something is not exactly as described; actual connections must diverge from what you think it is, or a faulty device somewhere.
It could not do what it is doing, if it is actually as described (or has a wire shorting or miswired or a device fault).
[EDIT]: Thinking this through more thoroughly, a ground loop would not explain the breakers tripping if the generator was wired wrong. This only leaves a load you overlooked, or a fault in the wiring. (speaking practically).
Make sure you don't have a main lug feed (terminology?) coming off the main panel buses, and connected to a load you missed.
If all your wiring checks out, the I would not move wiring too much or you may loose the fault you are trying to pinpoint (the problem could 'go away', only to appear again sometime in the future!). I would check the main panel buses and pool box breaker for voltage first (for safety), to be sure everything is off/isolated; then ohm all ways to see if there is a fault somewhere.
The only other (unlikely) possibility is if there is a defective breaker that does not open (shut off). You stated you are using double pole breakers (not 2 singles), so it should not be possible to stab them on the same poles...
[I would not rule out a main breaker that did not open one pole; however unlikely it could be possible]
Check and double-check...
Again, I emphatically second with Harper - Reinstate Monica and others have stated: You MUST have an interlock method!