I've made a test project that will reproduce the issue.
Basically any ui-boostrap animations cause Karma's navigateTo method to hang until the amimations are stopped or paused. So if you have a beforeEach with navigateTo, your tests will never run (unless you interact). There was a rather large thread over in karma-ng-scenario about this issue.
We should probably solve this by using ng-animate instead of the custom $transition service. But this won't happen overnight...
$transition is going away in favor of ngAnimate - this is happening very soon so closing.