I made a system with my quarry. Quarry output is put into an enderchest, which is put into a diamond chest, and that is pumped into my barrel system, like so:
But alas, all my barrels and my diamond chest are full.
As well as this diamond chest.
But I'm not an idiot. While I used Buildcraft pipes to pipe things to my barrel system, you will notice that I used pneumatic tubes for my barrels. So, where are my items!?!? Are they stuck in the transposer?
UPDATE: It looks like a chunk reset deleted all of my stuff. sigh.
Best Answer
I think they're landing on the transposer at the bottom of the pit, not getting pulled in because it's full, and despawning.
Really, this needs the BC pipes removed to work better, and there's no reason to start with a RedPower2 transposer, switch to Buildcraft pipes, then go back to RP2 tubes. Just use RP2 tubes throughout. That won't prevent problems when the Ender chest fills up, but it will stop this side of the system from leaking items.
To prevent the Ender chest from filling up, you really need more item overflow storage. There should be enough chests that you keep empty at the end of your tube system that they can store about half the entire quarry output, if necessary. I would combine that with an overflow just before it for just cobblestone (using a filter) that would redirect cobble you can't store into a recycler or an obsidian pipe/void pipe assembly, since you don't want your emergency overflow to fill up with cobble and render it useless.
To keep the overflow useful, always make sure to empty it before starting a new quarry.