We have the same issue, only difference is that we experience this with Cisco ATA191 that we are using for faxes. These have issue where they are dropping from the network and we have to power cycle them to reestablish their connection.

I am also trying to figure out way to list individual switches rather than stacked switches, this does not give us the actual switch count.

I am in a similar situation, few not all access ports report link downs on a regular basis and removing/adding snmp config does not help. Our reporting process is via CiscoPrime, could it be a Prime issue?.