Can you take a look into the queries kibana is doing in each case? You need to open the Inspect link in the visualization top bar and check both tabs for the Request and Response. You can actually copy the request into the Kibana Dev Console adding a GET /your_index/_search to execute the query on your own.
I'm thinking you may be hitting something similar to this scenario where time zone settings could affect the results, but for sure checking the queries and results will give a pointer on why Kibana is giving different results.
Hope it helps!!