I'm having the same issue except in my modpack there is no Thermal Dynamics
I have 6 blaze spawners captured from the nether using diamond dollies. After spawning into the trap, they are ushered into a pit of death (iron spikes). The vacuum hopper is sucking out the items (and XP) from the chamber....or...that's what it should be doing.
I resorted to Ender IO fluid conduits as I have often done these past few months. The redstone IS disabled on the conduit, btw.
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