Unfortunately CS4 cant handle H264 in a mov wrapper very well. They fixed these issues in CS5.
I you plan to keep on using CS4 i recommend Cineform Neoscene to convert the files in something editable and exportabel.
I’ve been using TMPGenc for some time now to get HDV to DVD.
For the intermediate file that i need i use NeoScene.
And i am very happy with the workflow. TMPGenc makes realy good mpeg2-dvd, i import them into Encore make menu and burn with Nero.