progressiveMauve Orthologs Output

[Adjuvant]

I'm aligning 9 prokaryotic genomes, 7 of which are annotated and two are not. In the manual, on the bottom of the Mauve Output File Formats page, it is intimated that if a positional ortholog in one of the genomes is found, but there is no gene annotated in that region, the ortholog will be output, but without a locus tag. My output is showing orthologs among the 7 annotated genomes, but none in the 2 non-annotated genomes. The alignment file that was simultaneously output is definitely showing many orthologs in those 2 non-annotated genomes. Anybody know how I get these to output in the orthologs file as well?

Thanks,
- A