Two separate things are happening here, and one of them you can fix today.
Tag shelves are scoped to the project type. Your mods link out to /game-mods/tag-farming-simulator-25, which holds 1,706 results. Your new tool links to /tools/tag-farming-simulator-25, which holds 7. Same tag, different shelf. Anyone browsing the mods section won't see the tool, however it is tagged.
Three of the tags on that tool return nothing at all in the tools section. farmsim, farmsimtools and fs are all zero results, so they're spending three of your ten slots on empty shelves.
The second thing isn't tagging. I checked Seasonal Calving, published 10 August, and it doesn't come back on a full title search either, with no defect on the page itself. That one is the indexing queue, and a support ticket is the only route to it.