I'd love to be able to help you out, but what you describe doesn't immediately suggest any problems to me. Would you be willing to re-create the problem in a small map and upload it?
i'll email you the map if u give me ur adress. find out first hand, more detailed description of the problem:
You finish an upgrade, weapon damage upgrade. The upgrades effect should be that all Units' weapons are upgraded, and so recieve 1 damage increase. (just like normal warcraft. you upgrade, and all units you already control get the upgrade)
What happens in my map: When you finish an upgrade, the units that you already control do not get the damage upgrade. Standard damage is 1-1, after the first upgrade 2-2. After the upgrade the units already ingame still have damage 1-1, but the units which are newly spawned, do get 2-2.
The upgrade itself works, but only applies to new units, units that come to existance after the upgrade is done.