Ok, I also posted this on the Google Analytics support forum. You'll find a lot of screenshots there about my problem.
The bottomline is that the original homepage in a A/B test receives far more 'new visits' then the variant. This seems to be the main cause for the orignal homepage to be the winner in the experiment.
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Has anyone seen this before? What could be the reason for the original page to receive more new visits? And shouldn't homepage A/B tests results not always be filtered by visits that only saw either the homepage or the variant (so filter on only 'new visits' that occured during the A/B test)?
Any input is much appreciated!