I was looking at one of my proposals, and my reputation counter is messed up. The top bar says 568, but the "proposed by" section says 793 and has 4 more bronze badges. How is this??
Your reputation counter is not messed up. It's working exactly as it should. Look underneath the "793" and you'll see an Area 51 icon and a Stack Overflow icon. The 793 is the sum of 225, your Stack Overflow reputation, plus 568, your Area 51 reputation.
In other words, this is your total score on Stack Exchange where all accounts are included where you have at least 200 or more reputation. Same goes with badges. You're seeing more badges because it includes both the badges from Stack Overflow as well as from Area 51.
As you increase your reputation score on other sites so that they go above 200, they'll be added to that total score whenever you make proposals or follow them.
Hope this helps!