Confirmed this a bug in the new plugin version (tracked back to a somewhat recent code refactoring that allowed support for a new feature - semi-silent deployment from a toolbar button or keystroke sequence).
The bug will only show itself if you've never run the export wizard before for the current instance of eclipse. Instances that have previously sucessfully run the export wizard at least once, should not experience this bug - hence RokuRob's previous comment.
I've got a fix, and am just awaiting approval to do the check-in (once that's done the same approver should be able to publish the new version of the plugin fairly quickly).