I have tried searching for pages which contain a particular tag, querybuilder of author instance is giving accurate results, whereas publish instance is not giving required results with the same query.
Note: pages and tags are replicated and when I search pages of other tags, they are working fine but pages of particular tag are not showing correct results.
Can you please provide the query that is used? I had noticed difference in results when looking with type cq:Page vs looking for jcr:content nodes of pages with given query criteria. May be this is similar issue
If not already verified, please check if the pages that are not coming up in the results have the cq:tag property set with the expected tag in publish crxde. If the tags are present on those pages as expected and you've not created any custom indexes, re-indexing on 'cqTagLucene' might help.