Hi Rotarrin, welcome to the forms!
To colonize a system, you need to
right-click on the ship icon in the task forces list, and a command list will appear. Colonize system is one of those options.
...If you're still having trouble though, it may be the game has glitched. Save your game, close it, then reload Supremacy. Load your game and see if it works. If it doesn't start a new game and see if it works. If it stil doesn't...you'll have to wait for Mike. With any luck though, right-clicking is all that your problem was.
Welcome to the forums.
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