Qualys is saying Authentication works with NTLM. I then get Links collected 30+ Requests performed 25+ and
Links Crawled 0, Assessment time 00:00:02
Why is Qualys WAS not crawling and such a short time when NTLM is being used?
Typically this indicates there is some type of connectivity issue between scanner and web app. Alternatively the web app is having problems for some other reason and is responding so slowly that scanner times out. I think if you have looked at possible connectivity issues and haven't seen performance problems from the app while running the app you should contact support to see if they can help.
It will be difficult to answer this without more information. If it is collecting links, but not crawling - then you may have a scope issue (none of collected links are in scope), a blacklist/whitelist issue (again - putting links out of scope), it could be some other setting - or it could be a bug. I think support is probably the best way to pursue the issue if you review all of your settings and can not determine the issue. They will ask for a scan report and test permissions.
Connection lost during ePhaseCrawl phase. What is this?
From the scan it says Links that timed out:
Retrieving data ...