Generally when you hit the left align, center or right align buttons it is centering everything inside of the content holder "div", "span", "table cell", "paragraph" or the like. What you will need to do is insert a new div below the flash header and then align the content in that div as you want.
Insert > Layout Objects > Div Tag
You will probably want to have a soft break first in between the flash content and the div by using [shift+return].
Abraham