it is also set to True:
> [galaxy@bic galaxy-dist]$ grep Ryan *.log
> runner0.log:galaxy.jobs WARNING 2012-01-10 22:17:26,381 Ryan Golhar - self.set_metadata_externally = True
>
> Clearly something else is going on here.  On my last import of BAM file, even after samtools finished indexing the BAM files, Galaxy never registered those jobs as completed.  So this problem is still there as well.

Thanks for checking these.  So, what does your server log for runner0 look like?