Well, first I am saying that a clean install works fine. Second, I am saying look into your registry or the Mids file structures for any files or entries you may have missed. Or just throw your hands in the air and give up.
If you let Belladonna escape and side with the Resistance you will not be able to do the Loyalist Power arcs (Dr. Hetzfeld, Bobcat, Neuron) until you do another morality mission and select the Loyalist option.
I still take Combat Jumping at 6, travel power at 14, and Hasten (if used) at 22. It is pretty much my build template for almost all builds. I do find the added attacks at lower levels a plus when playing a tank.