The gates sends a strong redstone signal now. It's like placing a lever directly on the machine instead of on a block next to the machine. Same effect. So, not bug in your end as such, I think.Use Itemducts. There's no need to worry with stopping machines or having anything overflow. That's kind of the point. Also, machines shouldn't be spreading redstone signal. I'll check and make sure, but that does not sound accurate.
I still prefer the BuildCraft pipes. I feel more in control then. The ItemDuct is a little bit too helpful
I might have found a bug with the auto eject on machines. It looks like they don't check if the inventory slot is valid. "isItemValidForSlot". The ItemDuct do, but not the machines.