There's probably a couple of reasons for the behaviour you're experiencing. But let me start by noting that I don't own a Q-filter and never used one, so what I'm saying just comes from general knowledge.

>"Or maybe it's as it was mentioned how the Q-filter prefers high output pickups?"

That's most likely one of the reasons. If you're playing over a guitar amplifier (speaker response up to about 5 kHz), you won't hear much difference. The 298 is probably the only pickup in your setup where the Q-filter can be useful over guitar speakers.

>"I'm using 2 250k pots right now, master tone, master Q-filter."

So, with a volume pot you have three 250k master controls now? That might be a bit too much load for the pickups, so that the resonant peak is dampened. You have a less characteristic sound then, and the effect of the Q-filter will also be less audible. You could go for a no-load tone pot, because it's unlikely that you'll use a conventional tone and the Q-filter at the same time.

Another option you could try is to use the Q-filter without the RC network, just like a cap on a tone control. I've heard from more than one user that this gives a more audible effect. I'm guessing that this is also a result of using guitar speakers instead of full-range speakers.
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