Placeholder while I get screenshots and write it up.

FWIW I just got a very simple "Dump chest" ->recycler->Mass fabricator system working. I think I can shorten it a bit though, the trick is to raise the fab off the ground so the pipe can go in underneath.

My tubes are overcomplicated at present and I think you can get away with 2 timers, 2 transposers and 2 tubes. You could use 1 timer and redstone wiring but it's not as tidy.
Place transposers while facing the direction you want stuff to go, so place the transposer first then the source machine.

From output to input I'd go:Place a tube and put the mass fab on top.
Place a transposer in front of the tube and place a timer alongside.
Place the recycler in front of the transposer and place a tube on top
Make a small platform so the last three items can be raised off the ground.
Place a transposer in front of the tube, timer alongside and a chest in front of the transposer.

Apply power and anything you put in the chest gets recycled and turned to uu-matter.

You can adjust the direction of transposers and filters using a screwdriver or sonic screwdriver, just fyi.

Thanks for the tip. Also I played around with it in single player and got it down to 1 timer operating 3 transposers, the third one was pulling matter out of the fab and into a chest. The whole lot could fit in a 3x3 square, with the recycler and its transposer sunk 1 into the ground. Place one redstone on top of the sunken transposer to link it to the timer.

Since then I've found I need scrap for fertilizer so I'm not actually running that config but its neat anyway.

Also I'm trying to figure out the "Buffer (tubestuff)" device. I thought it might output into tubes but it seems to need a filter. It will pulse the filter automatically though. [edit the buffer is recognised as a chest by industrialcraft, it outputs a weak redstone pulse at 5 second intervals if there is at least one item in it. (item sensor!). The weak pulse will not activate dust trails but will trigger redstone logic. ]

I think the item I'm looking for is the "relay", it accepts items from a quarry as though it was a chest, but pushes them out into a pneumatic tube. Oddly enough I tried to use it with a miner though and the items were spat out on the ground. [edit: because industrialcraft machines don't recognise a relay, buildcraft machines do]

To put this thread back on track:

How to make a leak-proof quarry using redpower pneumatic tubes.

1: Get the items into a tube:

You have a choice here:

• Use a chest to catch the items and a timer-transposer combination to output them.
  
• Use the above but with a filter instead of a transposer. This allows setting the timer to a longer period and tends to batch things into stacks.
  
• Use the Relay from Redpower. This will accept items from the quarry and output them into the tube. NOTE the relay is NOT compatible with the industrialcraft Miner or Pump
  
• Use the Buffer (tubestuff) AND A FILTER. The buffer is a chest with a built in redstone pulse to operate a filter. It is compatible with the IC pump and miner.
  

2: Prevent items spitting if it fills up:

For this you need an "Item detector". This goes inline with the pneumatic tube. Set it to its third mode, the one with the red "X". This outputs redstone when an item fails to exit the detector. Link this to your power source so the signal turns the power off.

• If you are using an energy link you could run redstone to it as a redstone signal will shut it off. Note the link is sensitive, so placing it next to the detector is enough
• You could install a "EU splitter cable", which is easier as it shows its state, it glows slightly when recieving redstone but its less sensitive and will need redstone between it and the detector
• You could configure a batbox to respond to redstone, it also needs at least one redstone between it and the detector
• If you are running the quarry from a buildcraft engine then you'll need to invert the signal from the detector, however you can do this by attaching a redstone torch to the detector, shift+right click to place.

In the event of items backing up the power will turn off, and there is enough storage at the quarry to catch any overrun while the quarry winds down. Collect some items to clear the block and it will restart automatically.