Ran some more tests. Looks like it's only happening with download monitor. It's no big deal, would just look a lot prettier if it didn't look the way it does. I could probably re-assign them manually.
Screenshot can be viewed here.
What I did was come up with a file naming system for all my media. I created placeholder images for everything before getting into the nitty-gritty of choosing & batch processing my photos (ie: create a placeholder image called foo.jpg, made it my feature image. Then when I'm ready I just replace my placeholder foo.jpg with the real foo.jpg in my uploads folder and voila, just like that, my entire site is populated with all the right images.
Might seem like a stupid idea but is working great for me so far, that is until I noticed this. ;)
Thanks Sean! You rock!!