Exporting to 720p HD MPEG-2 from FCP6

Hi. I have created a 30" animation in After Effects 8 (using the HDV/HDTV 720 29.97 preset) which I need to export to MPEG-2. This version of AE does not export to MPEG-2 (h.262) so I need to bring the movie file into FCP6 and then export to MPEG-2. I have exported the movie from AE using the Animation codec. In FCP6 my sequence preset is HDV-720p30. When I place the exported movie file from AE on the timeline in FCP6 I get a message saying the clip does not match any of my sequence settings and the recommendation is to let FCP change the settings to match the clip, which I've been doing. The only settings that seem to change are the editing timebase from 29.97 to 23.97 and next to Compressor, Animation shows up instead of HDV-720p30.

I have been exporting to MPEG-2 using Compressor, which I have never used before and have been following a procedure I found online. I've been dragging the DVD: Best quality 90 minutes folder from the Settings window in Compressor into the batch window for my video file. When I check the settings in Inspector I see that the selected frame rate is 23.98 and SD is selected for stream usage. So I've been changing SD to HD and 23.98 to 29.97 under encoding. I've been previewing the exported MPEG-2 file in QuickTime Player (I don't know if this is the correct way to preview the file) and it plays back twice as fast and jerky, apparently dropping frames. According to the QuickTime Inspector the frame rate is 59.96.

So I re-imported the AE movie file into FCP6 and this time did not allow FCP to change the sequence settings to match the clip. I exported to MPEG-2 using Compressor and previewed the MPEG-2 file in QuickTime. This time it played back perfectly smooth but still twice as fast. Obviously I'm doing something wrong and/or don't exactly understand what's happening in this workflow. Any advice would be most appreciated.