I explained this in a youtube video, which is much more graphic and understable. I link it here: https://youtu.be/lZlVouN2cBY
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Is this still an issue in the current Minecraft Snapshot 15w47c or later? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.
I have a similar issue! Spent ages designing and small scale testing my own little villager minecart transport system which basically runs in a circle from an infinite breeder through a trading system. Built the whole thing on a larger scale in survival only to have some of the activator rails fail to work properly every single time.
After a bit of messing around in creative I figured out that it seems to be specifically if the tracks are oriented east-west and you're trying to get the villagers to eject on the SOUTH side of the activator rail. Ejecting them on the NORTH side seems fine, as does north-south rails ejecting east or west.