Search getting inconsistent results

Having some inconsistencies with smart search results. When using the Smart Search preview window the results are accurate and as expected. But when the results are requested through the MVC method (SearchHelper.Search()) the listed results are incomplete and vary. We have 2 specific documents (example: red and green) with the same Page Type and same location on the pages tree structure. When we make the call to the search method on MVC one of these results gets omitted. Depending on the machine where this code is deployed (development or production), the results will omit one or the other as in:

Production Server => shows red but omits green Development Server => shows green but omits red

The behavior exists even for different page types as well and both MVC deployments point to the same admin and databases. We're on Kentico 12 SP Hotfix 99 with only one site in one language and the call is being done by the same user in all the setups. The indexes have been rebuilt several times and the documents have been re-saved as well but the results persist.