Hi Cody,
Just for case - what version of ITMS are you using?
May you please clarify your issue
Is your o365 software product detected as installed on 600 machines in ITMS console while you expect to see 5k?
or
Is you o365 software product is detected as installed on 5k machines but metering shows that is it 'in use' only on 600 machines while you expect to see greater numbers?
If it is detected as installed on 600 machines instead of 5k, please review Inventory tab of affected Software Product - only installed software that match all defined inventory fields(software name company version) will be detected as part of this product. These fields may be defined using rules(i.e. "|" = OR)
If you see problems in "In use" numbers, it seems that metering of Office 365 may be configured inaccurately on you setup. Officeclicktorun.exe is not file that may identify that office application is started. It is just updater/installer and it may run on background even when office application is not running at all and also it may not run when some office application is started.
to meter usage of office 365 more accurately you need configure metering rules for actual executables, running applications. In example - when excel is starting, excel.exe is running, so you may need to configure metering as " excel.exe 16.*"
If it is possible may you please attach screenshots of Inventory and Usage Tracking tabs for affected product. it may help to understand problem clearly..
Thanks,
Roman