Edges of logo in AI, EPS or PSD are not crisp (PE4, Illustrator CS2)

When importing files of the following types (AI, EPS and PSD), the logo I have placed still looks slightly pixelated/fuzzy.  Same thing goes for any title slides I have created in Illustrator and imported into PE4. I did outline the text before saving to the different file types.
I read this thread: http://forums.adobe.com/thread/390820?tstart=30 and tried the suggestion but it didn't seem to work for me.  I am working in 16:9.
Any suggestions?  I have a logo at the beginning and end of the video, and it is smaller and overlay throughout the video (watermark).
I am placing them at their proper size (example, for the overlay, I created the image in Illustrator, small and to the bottom right so that I didn't have to scale or move the location of the image once in PE4).
Many thanks in advance - this board has been invaluable to me.
Message was edited by: dmceathron - spellcheck :)

I may have misspoken in that thread, and not used the correct terminology.  I have no idea where I got the 960x540 number from, TBH.
The original size was 1920x1080, H264 codec.
I used SuperC to make them same size (just verified in WMP), using the FFMPEG encoder, which uses the CyberLink Video/SP Decoder (PDVD7) CODEC.
I used the preset for NTSC-DV-Widescreen for each project.
When I Interpret Footage, it tells me the PAR is square for the video clips.
I did scale everything to 102.5 percent to get rid of the very thin black lines to the left and right of the clips.
So I'm guessing that everything is OK with the files, project presets, etc, as the Flash output looks great.  The only issue is the title slides that I want to drop in.
So, I guess my issue now is, what size (dimensions) file do I create is PS to create a title that is properly sized for this project?  Do I go in and create a 720x480 file with the 1.2 PAR?  That seems to give me a more correct looking size?  Wow, I feel as though I have completely over complicated this question!
Print was so easy - this is my page size, I need a bleed, outline the fonts, I'm done!

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