The attached patch tries to fix some issues I have found, this may also be related to the ones mentioned earlier in http://www.spinics.net/lists/fio/msg04187.html
The part regarding stonewalled jobs may require some further work, but at least it gives proper values now for my standard fio runs. Sorry for not sending the patch inline, I'll have to get rid of using this *censored* web-mail interface for that. Also, I'm still wondering about the intention behind the way done_secs is being used. It cumulates time spent in finished jobs globally, but is being used in per-job ETA calculations. This seems to break at least for the case of stonewalled jobs, too.
patch
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