[SmartCrawl] Crawl/Scan results not getting through

When running a Crawl on my sites, the results show 43 URLs missing from the sitemap, even though the sitemap.xml contains those URLs. When running the Crawl from WPMU DEV end, the crawl completes correctly with all URLs located and none missing, but the data isn’t showing up on the site. Same thing happens with my other sites and other features in SmartCrawl – they can’t complete, time out etc.