Anyone have experience auditing with Nessus?

So I'm working with my IA people to audit our Cisco equipment, and it's kind of a nightmare. Nessus seems fairly straightforward but most of the time it just won't grab any information from the switches.

For instance, we have some Cisco 2901 routers with integrated switch controllers. They both have the same ACL. Nessus grabbed from like 5% of the routers but got like 70% of the switches. Other situations with 3750s we see a ton of traffic between from Nessus to the switches, but Nessus barely gets replies back.

We're positive that the login is right, just local logins. Its the same audit file we're using between the same devices as well. It's almost like Nessus logs in and just doesn't do anything.

Are there any tips from people with experience on this? Is there something we might be missing? We've played around a lot with Nessus settings to see, and even just gave it super simple scans to do and it returns with nothing.

Thanks!