The mirrors mostly update on the hour. Cvsuping less than an hour apart may be using the same old data. You need to wait until 15-20 minutes after the hour for the mirror to be updated. I mirror most of the data and it takes around 8 minutes for a mirror update to finish.
I waited a bit, then ran cvsup on the ports, once more, and this time there was more to download, including a new INDEX-5 file. I ran portsdb -Uu once more, and it worked perfectly. I guess my ports tree was out of sync somehow.
Thanks for the suggestions! :)
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