Okay, here's what's going on. Feel free to contact the NGG author about this, as there's not much I can do about the compatibility issues on my end.
The author of NGG is loading a custom version of the thickbox.js file and assigning it a unique queue identifier when loading via the WordPress script system. The issue is, I'm also trying to load WordPress 2.5 and 2.6 built-in thickbox script. When that occurs, you get overlapping boxes when launching a NGG image.
What I tried before was detect when the NGG script is present, and use that one instead of the built-in code. However, it's compacted code, and I can't call the individual functions without running into issues.
What I've done is detected the NGG script, deregistered it, and used the built-in WP 2.5+ script.
The problem that you are all experiencing is that the NGG author has modified the thickbox script for his plugin, but my plugin is disabling this custom version.
The fix would be, that I detect the NGG script, and use it. However, we're now back to the compacted code, which I can't use.
For those wondering why I need to call a function in the thickbox.js, it's for blogs that have 300+ comments. I'd rather have the thickbox initialize on a per-event basis rather than on the page load (a significant speed increase). So there's really no way I can get away with using a compacted thickbox.js script.
As of right now, there's no solution except either to a) leave everything as is, or b) deactivate Ajax Edit Comments.
Thank you all.