To increase the timeout setting on SNMP during discovery would be a normal, to get a proper discovery in CMCNE.
Especially if there is a busy management network or busy fabric where the switch is not able to communicate with CMCNE server within the 5 second timeout setting. We sometimes advise to set it to 30 seconds, it all depends on the environment.
Then I suggest you open a Service Request, and get this looked at properly via the Connectivity support team.
Suggest to collect the technical support information via the server management console (5th tab), also on the same discover screen in your screenshot, right click and "export table". and upload them to your SR for the TSE.