I had similar issues (works in browser, fails in phanotmjs) while doing integration tests on a website which used one of popular "twitter bootstrap" adaptations for AngularJS. It just didn't want to work (element wasn't created in time). I solved it by getting rid of 3rd party bootstrap directives and removing jQuery (which also was there). Then tests passed. TL;DR - do you have 3rd party code (directives?) there and have you tried testing without them
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