Did some more testing, facing walls: 60fps, facing crowd it drops.
That sounds exactly like in-game graphics quality settings.

Something to remember: ISBoxer virtualizes your Config.WTF file, meaning it has a different copy of Config.WTF for each Character you launch/play through ISBoxer. So when you launch a single character without ISBoxer, you may be loading it with different graphics settings than with ISBoxer. So make sure that when you're checking them, you do it when launched through ISBoxer!

You can reset any given Character to use the base config.WTF by going to your WoW\WTF folder, find the "Config-my character.WTF" file, and delete it. The file will be created from the main Config.WTF again when you launch him.