Hello,
if you turn on logging on the router you should be able to see the times the interface went down. Just make sure that you configure the datetime/uptime for the logging, the whole thing would look like this:
Router(config)#logging buffered
Router(config)#service timestamps log datetime msec localtime --> this shows you the logging entries based on the time the router shows with the ´show clock´ command
or
Router(config)#service timestamps log uptime msec localtime --> this shows you the logging entries based on the uptime of the router
When you issue the ´show log´ command, you should see entries telling you when the interface went down.
Since you are saying that you are using a network monitoring program: you can also have the interface send SNMP traps when the interface goes down/up.
In interface configuration mode, type ´snmp traps link-status´.
HTH,
Georg