Two switches, same hardware, same sw version, same snmp config - one works, one don't

Have you had a chat with support? Off the top of my head I would ask about the difference between the network paths between the collector and the switches. Have you tried doing a ping and SNMP GET from the command line (should be built into most Linux distros and there's a third party version you can use in Windows).  Should at least verify if the problem is LM or if it's specific to your environment.