Crafting Manager with buffer upgrade sometimes sends 2 sets of items

[Greg9711]

Logistics Bridge Version: LogisticsBridge-1.3.14

Logistics Pipes Version: logisticspipes-0.10.3.64

I have a Runic Altar automation setup that depends on the "Wait for empty inventory" function, it sends the crafting components plus one cobblestone to an input chest and the cobblestone gets pulled out at the end when the craft is finished making the input chest empty again so it can send the next set of items.
Sometimes (~33%) when the chest next to the crafting manager has all the items in multiple amounts it sends 2 sets to the input chest jamming up the system.