NOTE: This add-on is off by default. After installing, you can enable it without restarting Firefox, by viewing its settings through the Add-ons Manager.
A while back, Firefox Bug 615866 was reported. Firefox had recently been updated so that all links in an App Tab were forced to open in new tabs when clicked. Many people mistook this for a bug, but it was in fact a feature. Even though many people found that feature unintuitive, it was deemed a "WONTFIX": the feature was kept, and no offical setting was added to turn it off.
An unofficial setting will have to do, then. You can force App Tab links to behave normally by installing this add-on, viewing its properties, and enabling it.