While playing Sky Factory 2.5.1 when I disable channels I am unable to craft certain objects...So far I have found that Transfer Pipes (from extra utilities) and 64k Fluid Storage Cells (from extra cells) are not craftable.

When shift+click the "?" in NEI it takes me out of the crafting preview screen but it does not put the items in the crafting table. When I manually put the items in; I can see it in the crafting G.U.I but when I try to pull it out nothing happens. Shift+Clicking doesn't work either, and I cannot create a pattern for either item as well. The pattern simply will not encode when I click the button to encode.

are the original recipes (with enabled channels) working the exact same way ? or were they altered in some way? To be more precise, can you show us the recipes, as i am guessing theyy use components that no longer exist..

I believe they may have been altered by the creators of Sky Factory. That being said, I was running on a server, I just loaded it up in singleplayer for 1.5.6 and the issue seems to have been fixed, however the recipes are different now (I assume their original recipes)

disable channels on both client and server, see if that solves your problem, as the client uses items that may not be present on the server for displaying the recipes

ultimate resolution would be digging inside the configs to change the recipe to something working

PS i close this as this is a third party mod issue and disabling the channels is just braking a modpack but not an actual bug