Your screenshots don't really show anything relevant, so all I can give you is the basic behavior.
Redpower tubing gets clogged up when all valid target inventories for an item currently in transit become full 8and thereby invalid). The tubes will then "backstuff" the item, i.e. return it to the sender (in this case, your sorting machine). Only when there are valid target inventories again, the sorting will resume.
My guess is that whatever you're doing with the cobblestone, you have so much throughput that the inventory on the other side of the tube can't handle it. Recycler gets fed faster than it can recycle, chest fills up, or anything similar.