While doing the site audit here at work I've been using nessquik 2.6 and it's been chugging along nicely.
There was a peculiar bug that was occurring whereby the audit results on a /24 subnet would have all the IP address for that subnet listed even if there was no live node on the network. This turned out to be incredibly frustrating too as I knew it was a problem with my software and not Nessus this time.
So after a little while scratching my head, I tracked it down to nessquik not sending the appropriate values in the POST to Nessus to create the scan. It was resulting in none of the port scanners, or their associated settings, being provided to Nessus. So Nessus did the next logical thing and just decided to scan and report everything it could. The result is that you'd get these reports with lots of irrelevant information in them.
Well so I fixed that and now Nessus finishes scans much quicker. To the point where I almost cannot keep up with scheduling new stuff, which is fantastic.