Comment 2 for bug 249280

The reason this happens is because Nautilus switched VFS implementations in 2.22, from the gnome-vfs library to the GIO library. While this is a good thing, several applets in Awn Extras (including affinity) have not been ported to GIO. So, until these applets are ported, the launching application for files will be different between Nautilus and the applets.

For interested developers:
It would be ideal to preserve backwards compatibility for those users who do not have the equivalent of the Gnome 2.22 stack, so I discourage just throwing out the gnome-vfs implementation unless you have a good reason to do so.