Hi B,
Sounds like you have pages that get enough organic traffic that Google is pulling the price data, without schema markup, from the page content. If this info is clearly marked the google bot can pull it from content and associated with the search results. By adding schema you can take some control over this, but if the information you mark up with schema doesn't match what is on page it is a pointless exercise and will be ignored.
Out of curiosity has the conversion rate on these pages increased? I only ask because a reduction in CTR from organic search could indicate that you are getting more qualified traffic and a higher conversions rate would be an indicator. Basically having the price in the search results means there is no surprises for the potential customer when they click thru.
Posting the URL will help us troubleshot if you are comfortable with that.
Mike