Hi Simon,
I have the same problem and haven't fixed it a hundred percent. It seems there are two sources of those up/down-messages: traps and iMC-polls - as long as you defined a trap address on your devices.
What I did to get rid of the trap messages was to generate tables (unit1 to unit6 in my case) with excel and copied the result in text files (one per unit).
The text files look like this:
int e 1/0/1
undo enable snmp trap updown
int e 1/0/2
undo enable snmp trap updown
int e 1/0/3
undo enable snmp trap updown
I copy whatever interfaces I am not interested in from the text file block by block and paste them into my terminal session. This way no traps are being sent to iMC regarding link up/down.
Nonetheless I still get occasional messages from iMC with outdated up/down-alerts as long as I do not "recover" those alerts.
You could set the status of the interfaces to unmanaged in the iMC-SQL-Database, but that's a lot of work, too.
select * from imc_config.tbl_if_info where dev_id=258
order by ifstatus
and then change the ifstatus in the database
regards
Patrick