There seems to be bug when using log importer in Piwik 2.1.0
Basic set-up only differs by having
trust_visitors_cookies = 1
After importing the same package of logs on Piwik 1.12 and Piwik 2.1.0 turns out that on Piwik 2.1.0 there are no visits recognized as returning, while on Piwik 1.12 there are.
Please see this FAQ: http://piwik.org/faq/how-to/faq_190/
To increase accuracy of unique visitors detection