So, first let me say that it sounds like there is more going on to cause your scans to run very slow. It shouldn’t take more than 30 minutes to scan a single site, so 6 sites should still be dome in about 3 hours. Also, if it is going into the re-scanning phase after 99% then it is likely an indication of Read/Write Errors. At 50%, it is possible that the whole scan is being blocked by something else on the site and completely restarting after the first run through.
The first thing to try would be to open the Error Console in your browser while running the scan and looking for JavaScript errors. Taking a screenshot for me (after the scan has been running for at least a few minutes) might help me spot if there is something else wrong that I haven’t thought of.
If you want to focus on fixing this issue with the long scan time I might be easier to run the Complete Scan on just the wp-content or plugins, that way you don’t have to worry about it scanning all those other sites.
You can also send me any details that your don’t want to publish on this public forum directly to my email address:
eli AT gotmls DOT net