Almost all of our logic for App Canvas stuff is in the /components/com_jfbconnect/libraries/canvas.php file. The problem with multiple canvases is that Facebook sends a special cookie which is signed using the App Secret for the app. If you have 100 apps running on your site, we'd have to go through each one to see if we can decrypt the cookie from Facebook. Each check takes a lot of time (in the computer world) and can cause some issues. They may have improved the methods to detect things, but that's how it was earlier this year.
There are likely other things we could do like forcing the Page Tab URL to something like
site.com/index.php?fbPageId=1234 so that we'd know ahead of time, but again, more things we just haven't looked into. Additionally, we'd have to make an administration area for each Page Tab in JFBConnect which could get confusing as *most* users wouldn't use many/multiple Page Tabs.
Feel free to poke around that canvas.php file and see how we do detection of things, and if you have questions, just let us know!
Thanks,
Alex