Okay, I generated a loading report. The first row is the species from which we got typical results. The second row is the first attempt at the problematic species. The third row is the second attempt.
Judging by this thread:
http://seqanswers.com/forums/showthread.php?t=43256
None of these results look particularly good. Even the one that I thought was good appears like it might be underloaded. Granted, I don't know what typical values are, or how they might vary across techniques.
What should I be taking away from these numbers? Thanks