first of all: I know that this is not a extJS-related problem - it's browser specific, and occurs only with Chrome and Safari.
While developing Aloha Editor (http://www.aloha-editor.com/) we're stuck with flash videos from youtube: we use a TabPanel for our FloatingMenu, which will keep close to the block element you're editing. However, embedding an SWF object will cause the TabPanel to vanish behind the objects - it seems that z-indexes are completely ignored.
After googling for a while I've tried setting the SWF's position CSS attribute to 'relative' to be able to set a z-index, as well as setting it's wmode param to 'opaque' or 'transparent' - nothing works for me. IE and FF handle the z-index fine (without any modifications).