> somewhere between 2.1 and 3.0, the keyword 'distinct' was 

Oops, that was me. And it wasn't intended. I'm using this for my own
setups and apparently copied it to master when I added some other stuff.
Hope I didn't mess up other people's experiments. It's been in master
since 7 August 2014 already and nobody noticed.

Sorry for that, you can remove it again if you want. 
Lines 1280 and 1282 of scripts/training/mert-moses.pl .

I'd assume that your 32 entries of the n-best list weren't actually
unique, though, but a number of duplicates of the (two) very same
outputs, as "distinct" should simply avoid duplicate entries.

Here's a link to a related previous discussion on this mailing list:
http://comments.gmane.org/gmane.comp.nlp.moses.user/11097
You can try the parameter "n-best-factor".



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