I sent a normal minecart through one portal and toward another in the nether. The minecart landed inside the portal but did not travel through. I tried again, but broke the minecart and replaced it after it entered the nether. It then traveled through the second portal easily. This problem is caused, I believe, by minecarts (Maybe all entities, have not tried any others) not updating when they enter the nether.
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Duplicate of MC-5686.
Great. Fix it, and I will be happy.
I don't think this is a snapshot bug. The odds of that are low. I believe this is a carryover from 1.4, and will test it in 1.4.7 if requested.