A couple of other possibilities (some remote):
If there is a Quick Key for the site(s), it could be disabled.
Your antenna could be disconnected, or not firmly seated.
They may be using a frequency for the control channel that isn't marked as a control channel in the database and therefore was not downloaded during programming.
The site(s) may otherwise not be correctly programmed. (A lot of little things are involved, any of which could be an issue).
As a rule "Finding Control Channel" means you are holding on a talkgroup/system and the scanner is not receiving control channel data.