Hmm... it's really hard to figure out from your message what is going on in your mission... sorry about that... :-\
Do you mean that an AI group with an AI leader (allowfleeing 0 setting for all of them) does not move to their next waypoint, if they have a contact with enemy? Maybe they want to take out the enemy before continuing to next waypoint.
I'm quite sure you don't need to have 'allowfleeing 0' in multiple places for same units. That is not the problem I think, but it's wrong.
Please do write your messages in a bit more organized manner.
Example:
"1. AI group is traveling by foot to their next waypoint (open fire, engage at will + allowfleeing 0).
2. They have a contact with enemy.
3. They hide and do not move to their next waypoint at all.
4. When I give them a 'move' command, then they will move. But that's not what I want to do.
I want the group to automatically continue to their next waypoint. What is wrong with them?"
Is that what you mean?
One more thing... is the group in your command?