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...95% of the content is exactly the same), am I risking being penalized...
...some of the international sites are showing up before the .com site...
Could happen for any number of reasons. Google isn't to know that your .com site is your "main" English site. How could it?
If I were you, I'd make sure G doesn't index duplicates of your EN site. Either by using a NOINDEX tag on the pages themselves, using robots.txt to exclude dupe content, or "ethically cloaking" the page for robots such as G's in order to server-redirect it to the english .com site for particular pages (though this may make it difficult to get your int'l pages indexed well).