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Network Atlas doesn't correctly display device links

I've already viewed the ConnectNow tutorial, and I'm doing things correctly.

I have a nightly discovery of over 400 switches and routers on my network. When I use ConnectNow in the Atlas, it appears that in many places that are physically looped and have a spanning tree blocked port, one of the connections is either missing or incorrectly connected back to distribution/core.

"sh cdp neighbor" shows both access switches directly connected to their distribution switches and to one another. Access1 shows the port connecting to Access2 in a blocking state. This isn't an isolated occurrence. It happens all over the network. Anyone have an idea about a solution?

Thanks in advance for your help.

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