(Apparently the Gmane web interface turned my reply into garbled text, sorry for the double posting)
Thanks again for your quick answers. Yes, 32 and 2 are the counts after "sort | uniq | wc -l". The total number of hypotheses returned for both cases was 50. I removed the "distinct"s from (my local copy of) scripts/training/mert-moses.pl (lines 1261 and 1263), and that solved the problem! Now I can get 32 unique hypotheses with v3.0, too. In fact, I am pretty sure I was able to get 50 unique hypotheses (out of a 50-best list) with the same configuration back in version 0.x. I hope the new -n-best-factor will do the trick. Best, ED
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