The campaign AI in Tides of Darkness and Beyond the Dark Portal (and Starcraft for that matter) was based on a "trigger" system. To keep the missions from being too overwhelming, certain enemy bases would remain on standby, just sitting around mining, until a certain condition was met which would activate them. Normally this condition would be moving your units past a certain point. A great example of this can be seen on the last Human mission in Tides of Darkness: Black only "activates" when you move out into the northeastern portion of Orange's former base. If you never go there, Black will just sit there mining all mission and not do anything (a great way to cheese the mission, by the way).
So it's possible that you just never activated the trigger. Unfortunately, I don't know of any way of being able to dig into the maps themselves to find out what the triggers are - AFAIK most of what we know is based on trial and error. It's also possible that the trigger was somehow broken. Sometimes restarting the mission will fix things.
It's possible that it got broken in whatever tinkering GOG did to release it, but I know that even in the original version there are issues like this. I think it's mostly just a weird byproduct of the way Blizzard programmed their AI back then. It tends to be more obvious in BtDP just because most maps there involve you squaring off against 3-5 different factions