From what I've noticed in my work with both BC pipes and AE buses, stats are indeed a factor. For example, in my Wither Skeleton farm (Soul Shard), the diamond pipe took durability into account when filtering out the stone swords. I found that I needed to collect each possible durability that a W. Skelly could drop and put that into the filter. After about six durability levels, the stone swords were properly piped into the void pipe.
Same thing with ME systems. Currently, I'm running apiaries, but want to switch to automated alvearys (which is why I'm here at all). I found that the difference between an un-analyzed bee and an analyzed bee made for more exact sorting. The un-analyzed drones (piped into a chest to act as a bridge for the ME system) were brought in and sent to an analyzer, where they came out with their stats intact (heavily modified so that all bees had the same stats, took FOREVER to inoculate). Those analyzed bees were then exported to the genepool for mashing. Worked quite well, but my comb production was crap, and of course, I couldn't automate frames.
So I'm thinking the "missing princess" problem could lie within the difference between an un-analyzed bee and an analyzed bee: Both the ME buses and the Buildcraft Pipes with filters (diamond and emerald) recognize the difference between things like durability and whether or not the bee's stats are known.
My solution is to have the ME network pull out the un-analyzed princess, send it to an analyzer devoted strictly to them, and then pull them back in to be sent back to the alveary. I haven't put this solution into practice yet, but reading this thread has led me to that possible conclusion. I'm going to test this theory after lunch today, and I'll post here with my findings.
ADDENDUM - Yes, it works. I set up an Alveary in my test world, and it did indeed export the bees into the Alveary. The trick is making sure you have the exact same bees every time - no mutations (stats or otherwise). You can ensure this by inoculating the original princess and drone with the exact same traits from top to bottom, guaranteeing the same bees each breeding cycle. This will result in a fully-ME-automated Alveary.
PPS - Grrr. Princesses still get stuck in the ME system. Thought I had it there for a moment. It doesn't even want to export them to the Analyzer. I'm not sure if the Alvearies do something to the Princess to mark it as different - these are fully inocculated bees that have been bred for generations upon generations. Still working on it...
AFTERWORD - Er. Mah. GERD. Got it working. Granted, it's not pure ME, but it works all the same. First of all, tune the ME Export your analyzed drones. This will keep it full and ready. Then tune the ME Import to pull out any combs and items that may be produced, as well as un-analyzed drones. After that, all you'll need is an Emerald Pipe, another pipe of your choice (I use gold), and an Autarchic Gate. Set the Emerald Pipe to pull out an un-analyzed Princess, and then put the gate on it. The pipe only seems to work if the product cells are free of drones, which the ME Import handles, but it pulls out the Princess and feeds it back into the Alveary for the next round. I'll be recording a tutorial video on this (finally!), so I'll post the link here once it uploads and processes. FINALLY!
Tutorial Video Link
