You have noticed that under "Licensed Programs" section of Resource Manager doesn't show all Software if those are set to "hidden" in Add/Remove programs on client machines.
ITMS 8.x
Inventory Solution 8.x
By default, we do not show any software that is set to "hidden" from Add Remove Programs.
If you need all software to show, regardless of the state in Add Remove Programs, please walk through this process.
Note that any repair or upgrade will revert the changes and they will need to be done again. Make sure you have a backup of your database as a precaution.