Sorry for the delay!
Actually I can't reproduce this on e.g.
http://www.managingpaintogether.ca/. The structure within the HTML panel stays open after inspecting the embedded SWF.
There was one related problem fixed lately in
issue 7469, which will be released with Firebug 2.0.5. Does the
build attached to comment 16 there fix your issue?
If not, please provide a
test case, so the problem can be reproduced.
Sebastian