Alright, here goes: I had a setup with my mass fabricator that would automatically pump scrap into it, through one of Zeldo's insertion pipes, such that when the mass fabricator was full, the next piece of scrap would go through a Redstone pipe and activate a mechanism which, to summarize, would turn on the mass fabricator long enough to use up the full stack of scrap, then turn it off again. With v. 1.23, the device worked perfect, and the MF was only on when there was scrap to burn. Then, I updated to v1.337b, and the MF got fixed so that it worked with Buildraft pipes in a logical way. I had to change my system around a little (connect pipes to the right faces), but the concept was the same. In this new version, the insertion pipe is underneath the MF and the wooden pipe pulling out UU-matter is on the right; the glass fiber cable is coming in from the back, and the redstone signal is from the top (with redpower wires). Sending scrap through the insertion pipe fills up the MF just right, but once there is a full stack of 64 scrap in the MF's lower slot, the next item to go through the insertion pipe vanishes instead of going down the fork to the Redstone pipe. I believe that it is somehow being "overstuffed" into the mass fabricator, but I don't know how that could be possible.
On a somewhat-related note, does a full MFSU with a redstone current still emit any "overflow" power it recieves? If I could set it up so that the mass fab is running off of my excess power full-time, that would make this strange glitch irrelevant.