In nested recipes using the same machine, it sends items in completely random order. For example, I have one recipe of Y that requires X in order to proceed, and a second recipe of X. It sends the materials of X & Y at the same exact time, result in neither recipe getting crafted. This is my current setup for reference. I have not a clue why the pipe is red by the way. It works fine.

My suggestion would be to rework it, so all of the required items are crafted and available, before sending the items out for craft. So if X requires Y and Y requires Z. Then Z is crafted and finished before any of Y is sent out, and Y is crafted and done, before any of X is sent out, so on and so forth.

It also seems to sometimes miscalculates the materials needed.. but this could just be the result of me having to rearrange the items as they come through and messing up somewhere

In version 1.1.0 items are only pushed out of the AE Bridge, if all of the items are crafted by the AE system, this does not check the Logistics Pipes crafting recipes though. Logistics Pipes crafts X and only asks the AE bridge for both input items, and sending them at once. This is an issue with Logistics Pipes, it sends crafting ingredients as soon as they are available. In the future I may add a Crafting Buffer Pipe to the Crafting Manager, so it keeps the items in a chest before sending to prevent this.