Please help!!!!!!!!!!!
I can't capture any of the rebel supply bunkers WHY!!!!
This causes a problem when trying to gain command points!!!

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Are you sending your troops inside of the bunkers? (Shift Right-Click) They have to dispose of the rebel troops inside of the bunker. Once one of yours is inside, click on the bunker and you can watch their health.

I had a similar problem, until I realized that you have to pay close attention to the animation of your cursor. When the building is selected, the cursor changes to a circle with an arrow. The default (i.e attack) shows the cursor pointing due north, while pressing shift to command your troops inside changes the arrow to a N-NW direction. Make sure your cursor changes; sometimes in high lag situations the cursor won't change and your troops will just stand there attacking. Also, as mentioned, make sure you have enough firepower to take out the rebels inside. And don't get too addicted to that steady flow of command points- some levels coming up soon have no bunkers (or a way to order reinforcements, for that matter!)