I think I found the problem; it actually wasn't ImageMagick's fault, nor was it anything incorrect with my MediaWiki configuration for it: It's that the installation is still using old thumbnails, and doesn't update them with the ImageMagick settings. I realized this when I looked at the file path for one of the thumbnails, tried renaming the file, and noticed that the server didn't regenerate it.
It looks like I won't need any fancy configuration options or setups after all. Lacking a better option for regenerating all the thumbnails, I simply deleted the thumb directory, and that seems to have set things straight. Not quite the solution I was expecting, but it's a solution nonetheless.
Very little to do with either emus or farmers!