[[MediaWiki:Newuserlog-create2-entry]]

I don't understand? Did you have local override?

Yes, there was a local translation that I deleted today; but that is irrelevant (that's when I discovered the problem, however). The message was translated here long ago, but does not appear on the wikipedia. Instead, the English source message appears. You can also compare the German messages: Wikipedia - Translatewiki

MessagesEn.php has a comment "do not translate or duplicate this message to other languages", I guess translation should be disabled here?

The message key is already in $wgIgnoredMessages of MessageTypes.inc. I do not understand why the message is translatable :-/

Probably because it's still present in branch 1.18. Once support for 1.18 is dropped that will be resolved.