It's possible to fix this problem. By default, the z-index don't work fine with Internet Explorer 6, you must set "transparent" or "opaque" the wmode parameter.
1) open up flowplayer-3.0.6.min.js
2) search for: object width="
3) replace with object wmode="transparent" width="
1) open up flowplayer-3.0.6.min.js
2) search for: object width="
3) replace with object wmode="transparent" width="