First off, awesome tool!
I may have found the answer.
If you track one domain sub directories or pages in different Piwik websites
By default, Piwik uses only one cookie for a domain name, all its pages and sub directories.
In the case where you track a subdirectory in its own Piwik website, if a visitor visits more than a few sub directories, this will cause some inaccuracy in a few reports: Time on site, Count of visits, Conversion referrer, Returning and new visitors. In this use case, you can ensure your reports stay accurate by creating a different cookie for each sub path you are tracking in different Piwik websites. The function setCookiePath() is used to set the Cookie path.
For example, if your website has user profiles, you could track each user profile page analytics in a unique Piwik website. In the main domain homepage, you would use the default Tracking code.
tracker = Piwik.getTracker(pkBaseUrl, X); // idSite = X for the Homepage
In the /user/MyUsername page, you would write:
// The idSite Y will be different from other user pages
tracker = Piwik.getTracker(pkBaseUrl, Y);