AHA! I have figured it out. Ok, here's the deal for anyone who should have this issue in the future.
The one frame thing was, I needed to choose the option to embed the video when I imported. That gave me the option of an expanded timeline.
Here is my process:
1. Using Flash Video Encoder, convert .WMV to a .FLV maintain appropriate file quality.
2. Import .FLV into Flash (CS3); follow steps but choose embedded video with expanded Timeline.
3. Adjust stage size and center video.
4. Import Sound to Library.
5. Add layer above Video layer (for the sound).
6. With Sound layer selected, drag Sound from Library and drop it on the Stage.
7. Save Flash file.
8. Using File > Export, save file as a .AVI at the best quality.
9. Import the .AVI to your web-host and Re-Encode as usual.
Yeah! I like it when things work. :)