Hi,

firstly ensure to have it updated based on this forum post: http://storejextensions.org/forum/view/10-jsitemap/5406-update-to-jsitemap-4-1-for-joomla-3-6-1-required.html

If you have a large sitemap and server timeout occurr, you should consider to use the AJAX precaching generation for the sitemap.
Generating the sitemap using AJAX and incremental steps will avoid server timeouts, this makes possible generate sitemaps also with 100000 links.

Remember that you need to handle XML sitemap not HTML.

As another strategy you could also export a static big sitemap positioning at server root as sitemap.xml and use the dynamic sitemap generated in realtime only for recent items.

Don't rely on the links reported as indexed in GWT. If your site is not new it reports only the difference of links added using sitemaps. Looking in the pdf component documentation is explained how to check the number of real links added to Google index using Google search.

Hope this helps.

Best regards

John Dagelmore