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One (possible) situation that accounts for some of the discrepancy is the way that email security programs work. Something like Kaspersky (or most server-level security programs) basically "click" all the links in an email to quickly determine whether or not the pages that they are directing to contain malware / phishing attempts.
Google analytics, on the other hand, can filter out these bot sessions at the host name, and most don't even hit the time threshold on page to count as a session entrance.
For what it's worth, my MKTO report and my internal server logs for the pages that the emails direct to are almost always wildly out of sync - and I doubt there is much that Marketo can do about it - since the variety of email clients, security restrictions, text vs. HTML rules, etc. is bewildering.
That was our conclusion too. When we looked at the activity logs of the Lead records that had "clicks" but didn't have page visits, the email delivery and email click occurred at the same time in the activity log. I also contacted one of the people that was in the group of leads that "clicked, but didn't have a page visit" and the lead indicated that she never clicked our email. This means that the Click data in the MKTO email link performance report requires a filter of "visited web page" to make the click data accurate.