BandonRandon - thanks (as always) for your help. A few troubleshooting issues:
1. With your test blog (which is not working), which is in a subfolder, what is the canvas callback url? (The setting in the FB app which tells it what to call)
2. Also, in that same blog, what do you have set in the WordPress side for Settings->General->Blog address and Settings->General->WordPress address?
3. Finally, are any other settings different between the two (requiring email address from comment authors for example? allowing anonymous comments?)
The point of the callback handler is to make it possible to have WordPress installed in a subdirectory, to move or rename the wp-content directory - basically to eliminate all assumptions about relative paths between the plugin directory and the wp-includes.
Doing it the old way required "guessing" about the path from where the comment handling form is to where the core wordpress classes are and calling them as an include - which is a bad practice.