After a great deal of time, I realize that my concerns from yesterday were incredibly naive. I was concerned because my detections were no longer strong, and I thought there was an invisible bug that magically appeared in my code.
I realize now, though, that this was never the case, and my "working" code was not as strong as I thought. The detections are weak, which is why we were originally going to change the smoothing filter. The only reason I got a chunk of strong detections at the end of last week was because I ran a larger simulation. These galaxies, which are between 1-2 kpc in half-light radius, are incredibly stealthy, and thus hard to detect given the original search parameters. So, when I run small simulations with only 5-10 repetitions, hardly anything, (or nothing at all), pops out.
In other words:
CONCLUSION: In order to truly test the detectability of AndXIX-type galaxies around the Milky Way, the search parameters need to be changed. This needs to be done carefully, however, because when we tried this last week, nothing changed.
I will not detail the amount of stupid things I did this morning to come to this conclusion. Let's just say when you svn "revert", you loose a lot of stuff. However, I think it was good for this to happen, as frustrating as it was, because now I have a deeper understanding of the search algorithm and how it works.