Thaumic Wonders has a multiblock-like structure called the primordial accelerator to convert primordial pearls into primordial grains. With ThaumcraftFix installed, the accelerator will consume the pearl, but not output/drop any grains. Without Thaumcraft Fix, the grains drop as expected.

This is probably because the accelerator checks the primordial pearl's max damage with Item#getMaxDamage() here, but TCFix sets the max damage of the pearl to 0 here. This is probably a similar situation to #53.

The structure looks like this (Primordial Accelerator -> Tunnels -> Terminus), and upon inserting a pearl in the accelerator and giving it a redstone signal, grains should drop at the terminus.

You're correct, this is the same thing as #53. I'll be adding a config option to not apply this fix.