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It's really hard to say, and it's definitely not unheard of for rankings to vary wildly between search engines. It's possible that you lost some ranking power when you nofollowed those links, or that Google is just trying to figure out where to rank you now that your link profile has changed. It's also possible that it's completely unrelated. Honestly, that's why I recommend the Full SERP Report—it might help you work out what it is that's letting the sites ranking above you pull ahead.