There have been other reports of taxonomy fields not loading and saving correctly. Most of the time it’s something to do with other plugins or a filter in place on the field. In one case the filter that was causing the issue had nothing to do with the taxonomy field (http://support.advancedcustomfields.com/forums/topic/okay-why-are-my-custom-taxonomies-not-saving-anymore/)
Try deactivating plugins and changing themes.
