Sequence Settings - Animation vs NTSC compression

i'm currently in the midst of editing a corporate video project for a client, who offers internet-based services. one of the videos i will deliver is a film comprised of 12 scenes; in the most important of the 12 scenes there is a woman that goes onto the client's web site. i shot the actress in front of the computer and the web surfing was recorded with the software ishowu.
now, here's my dilemma: the highest resolution video with the screen animation has the "compressor: animation" setting / 23.98 fps. The footage with the actress is NTSC video, 23.98 fps (DVX100 / frame pulldown removal process). and the two just can't go together. if i put the web site screen capture video onto the 23.98 / NTSC sequence, the quality goes down dramatically. If I change the sequence settings to "compressor: animation" Final Cut keeps crashing.
Any suggestions on what to do?

David,
Thanks for the helpful answer.
To address one of your points: the video will be first shown at a trade show, on a huge HD plasma screen, and will also be delivered on multiple DVDs for the client. The trade show is a high profile event, which is why I don't want to take any chances with such compression issues.
Whenever I use the DV/DVCPRO NTSC settings, the picture gets blurry and visible noise comes in at around 8-9 seconds into each capture.
Before iShowU came around, I wonder which software production houses have used to capture screen / showcase products.
I have a small arsenal of video software at my disposal (Final Cut Studio, After Effects, and a small army of other goodies) and can pretty much re-size, crop, re-compress, color-correct anything, provided the right tools.
One thing that worries me even more than video screen capture on a mac is the same thing on PC. One of the client's services is video on demand downloads, which is only Windows-compatible. I have yet to find a good solution (besides AVI-only tools) to the same dilemma, since I need to record the screen as I start downloading a video from my SO's PC. Any suggestions on that would also be greatly appreciated.
The project has a modest budget set aside for unforeseen issues, so I wouldn't mind buying extra software, if it turned out to provide excellent video quality.
cheers,
Elena

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    ok here's the info everyone has been asking for -- and, please remember, I have solved the exporting QT to make a DVD now . . . .
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