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A couple of months ago we had the same problem with 90% of our websit, due to the fact that our dynamic pages use Isapi rewrite. The implementation was of such a poor and awful quality that the construction of the pages took so long that Google always received a timeout when spidering our pages. The time to parse the pages might be a factor.
You might sign-up to the Google sitemap project and use its statistics to analyze errors returned from Google when spidering your site.