The description for mission 3 still mentions that upgrade points are gained through skirmish.
Also, I can't make as many upgraded parts of that tier or under. Once I get two parts of that tier +1 I can't upgrade anything. When I click the upgrade button for any part it tells me, "Core can not handle any more over-upgraded parts." I'm assuming that isn't supposed to happen for parts that have never been upgraded.
Yep, description for mission 3 was patched 10 minutes before reading your post XD.
Checking for your problem, it will be fixed for next version. Currently, i upgrade with the "U" button ( a personal shortcut to speed up testing) . Maybe theres a difference between both codes ? Anyhow, i'm sure U works, so you might as well go with that for now.
EDIT : Damn, i fail, U doesnt work either. Fixed for next version, you'll have to stay at 1 overupgraded part to avoid any problems for now. Sorry.
Edited by tabc3dd, 15 November 2010 - 07:52 PM.