The cmk -I hostname is not done regularly in a short time interval. For the normal check of your device only the really needed OIDs are pulled.
A a runtime of 1-5 min for a discovery run is long. The biggest difference is that your manual snmpwalk is not pulling all the enterprise OIDs automatically.
To inspect where the discovery takes so long da a cmk --debug -vvI hostname Now you see at witch point it is slow or waits some time. Write down the OIDs and then you can grep over the folder ~/share/check_mk/checks to search for a check that uses this OID. This check type can be disabled if not needed with a WATO rule.
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