One of the things I find most frustrating about Flash CS5.5 is that checking the "Align to Stage" check box in the Align panel seems to yeild results that are not even remotely what I was expecting. For example, if I want to center an object on the stage horizontally and I have this box checked, the center of the object will align with the left edge of the window.
A quick fix I've found for centering objects on stage is simply to cut them and paste them back in. Unlike other applications, Flash doesn't paste objects at the coordinates where they started, but in the center. To paste them at their original coordinates, use Paste in Place (Ctrl-Alt-V). I normally find this annoying, but it turns out to be a great workaround to a feature that doesn't seem to be working correctly.
Is this fixed in CS6? I don't know, but I should be installing CS6 today, so I may update this post later with the answer.