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you should be able to choose which program is assigned to a specific file type. an easy way to do this, in windows, right-click on a file, "open with", browse to choose the program, then check the "always use this program to open this type of file." and select ok. you can still use different programs if you want (by opening them from inside the program, by dragging them onto the program icon, by using the same process "open with" again, even if you don't check "always"...) but a double-click on the file will always open it in the program you have specified.
logically, you should also be able to tell mobipocket *not* to make itself the default program for other file types, if not at the time of install, then in the preferences, but i have not checked this.
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