Compression Setting Question

This is kinda weird and I am hoping someone with a little more experience can give some advice. I am getting some hiccups in the preview video (FLV) and stutter on playback. The main HD file plays smooth as silk- just getting this on creation of the preview for the video- check an example out here: http://videohive.net/item/timelapse-storm-clouds/117141

First off my work flow for the time-lapse is as follows:

1. 525 image shot with camera at 3456×2304 2. Import sequence into Quicktime to render the MOV H264 output at 1920×1080 & 1280×720 which both of these files play very smooth 3. Open AE and import the MOV created in Quicktime and overlay the Videohive watermark 4. Export to 640×360 (and I have tried both FLV export and avi) when I have exported to avi I use Sorenson compression suite with the F8_HQ VP6 Pro settings

I must also say that when I have just shot straight HD from the Canon 7D and taken the RAW MOV file created using the process described above- bringing into AE, overlaying the watermark etc. the results are just fine as seen here: http://videohive.net/item/glistening-reeds-02/113412

Thanks for any advice or help

Ok… I think I may have found a decent solution using AE to export directly to FLV using a custom compression settings straight from the image sequence… If anyone still has any tips please feel free to share. Thanks