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Back from the active_tags, it seems Boostrap added special process to autocomplete tag field. I tried to fix it myself but I can't see any js exception or any hint there. One first error is the add button of acitve tags is wrapped to next line by boostrap.
https://www.drupal.org/files/styles/grid-3/public/images/active_tags_aft...
If Active Tags works with Zen, Adaptive Theme, Omega, and other popular themes, you probably want to submit a ticket with Bootstrap about it. If you can prove Active Tags doesn't work with other popular Drupal themes, then it should be an Active Tags issue.
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Comment #2
markhalliwell