nope, you're doing it right, as far as I know, the 'income lost to underdevelopment' designates the time you have red, negative income from a freshly colonised planet. the first pop upgrade should really be ordered as soon as the planet is colonised, because otherwise you have a big drag on your econ. bigger planets also require a second one to get you completely out of the red numbers, so that's a priority too then. the rest is up to you and your requirements.
so ... if you let seveal minutes pass between colonisation and the first upgrade, then maybe that's the problem. the only thing I can think of right now.