Maniac has a point. That could probably be due to the different profiles google sets in different browsers. I only noticed the difference when I am using different IP, and between logged in and logged out on any google service.
Are you logged in to a Google account in one browser and not the other, personalized search can throw up differences.
Download a portable version of Firefox or SeaMonkey and use a fresh copy every time you want to check site positions in searches. That way you don't have to flush all the cookies from your day-to-day browser.
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