What I know about Flex2 and the sidebars is that if you do not do anything with the top module, the categories and archives sections (as written from the sidebar.php page, NOT the widgets section) will apppear.
That's why it is suggested to include an empty text module to the top sidebar widget module. For some reason, this will eliminate the categories and archives section.
Understand that you can still have them there, if you want them, by using the widget modules instead of the coding that sidebar.php gives.
However, in some freaky cases, adding the text module to the top sidebar widget does not help. In those cases, I recommend cutting the coding that delivers categories from the sidebar.php page.
I say all this, not knowing whether this is even in the realm of what you are asking, because I am just not sure what it is you want, sorry.
~cj