Exporting as .mov

Hows it going folks. Ok I wanted to export my Flash movie as a Quicktime .mov. Kept getting that error message at the start but upon further investigation on the macromedia site I discovered that it need to be converted to a flash player 4 file as quick time currently only supports flashplayer4.

Anyway I did that and it worked however it has caused problems with how my animation plays which I am assuming is due to the F.P4 conversion.

Can anybody help me with this problem. Surely all Flash movies arent converted to F.P 4 inorder to play as .mov?

Thanks