Same issue having forced it to run in Java 1.7.0_45 (took me a while to figure out how to do that, what with apple not supporting/pushing java updates anymore.
Attached requested crash report.
With a little more research and talking to another player:
his version (same server, same minecraft version) does nothing when you click outside the sub-window, the crafting sub-window stays up
in my version, you can also click out of chests in a similar way (click outside the sub-window), and the chest block looks like it stays 'open' but the window goes away just like the crafting window goes away (for me).
I seem to have the same issue in 1.7.2 - though mine will generally go farther.
My dropper column seems to drive/push items through ~19-20 transfers, but no farther.
I took items out where they got stuck, and put them back a few droppers earlier, and they got stuck the same place - however! - when I inserted a new stack of material a few droppers farther along than my original 'start' and the new stack got transfered that same number of transfers and stopped at a later point than the original stack stopped.
I have dug out and verified the direction of all the droppers multiple times, as well as the redstone signal.
(oh, and I've also tried a bunch of different 'clock' speeds of redstone pulse to drive the droppers, I'm currently using a very slow one just to make sure that speed isn't causing this issue.)
Problem persists even when using newest version of java. [new crash report attachment added]