Graeme,
We're looking into adding an option to the Facebook configuration area to use an alternative OAuth flow. That new flow should work with your App how you're using it since it uses redirects to perform authentication instead of the Javascript popup.
That's something being investigated for the v5.3 release, due out in early next year. If we implement a solution before then that is easy to implement in the existing code, we'll post it back here for you to try out.
I hope that helps explain,
Alex