When I upload a new PDF-Version, the generated thumbnails from "Version 1" always shown. The Version 2 thumbnails are not being created.
Topic on Extension talk:PdfHandler
We had this same issue and tracked it to Semantic MediaWiki. If you have it installed, you can test this by disabling enableSemantics(). Tested with SMW version 2.5.8. See also the likely related topic here.