It seems that while a basin will show an output tube for a funnel, it won't actually input into that funnel. Worse, the output tube will stop the mixer/press above it from operating.

It's a downward facing funnel, and it just goes into a chest. Here's the sort of setup I have:

The mechanical press does not activate at all.

Confirmed that funnels do not work in 0.3.1c+151. Chutes on the other hand do work as expected.

So on investigating it appears that in order for its internal output buffer to have a valid output, it tries to ensure that the tile entity it is interacting with has an ITEM_HANDLER_CAPABILITY, which funnel tile entities do not. As such the acceptOutputs function of the BasinTileEntity will always fail. As the output attempt fails, the apply function of the BasinRecipeclass returns false which is why the machines don't activate.

So from here a fix really depends on what one of the primary contributors believes to be the correct behavior; should basins even connect to funnels not attached to their sides but rather on the horizontals a block below, and if they should should the acceptOutputsInner and tryClearingSpoutputOverflow function have a check for the special case where a funnel is attached, or should funnel tile entities have an ITEM_HANDLER_CAPABILITY added to pass the check.

For clarification is it a downward facing funnel or a side facing funnel? Also are belts involved because it could be related to the bug where side funnels attached perpendicular to a belt won't take in items if the belt is stopped, or could simply be a matter of the funnel not being able to output due to an itemstack on a belt below.