Fixed...
So I believe the problem is fixed, however I'm not 100% sure what fixed it. Here's what I did:
I deleted the plist file on my dropbox, I rebooted my computer and booted off the recovery partition. I reset my ACLs on my account and also ran a permission repair in disk utility. After that, rebooted back off the main partition and launched ARD. The first time it just opened like normal. I quit it and reopened it. This time, it displayed the license agreement as if it has never been configured. After clicking next, it asked for the ARD password. Entered that and clicked next to a few more setup questions and everything was back. Even my list and all settings. I was then able to make changes and they stuck. I also noticed I did have an updated plist file in the new location. So not sure if it was the ACL reset or the permission repair, but things appear to be back to normal now. Haven't tried re-creating the dropbox sync yet with the new location of the plist. I'll try that next.