Thanks for the report @phoob - it does look like a bug and we haven't heard about this otherwise.

Does anyone else experience this issue?

Seems it might be related to the fact that I used jQuery Waypoints to track events (when user scrolled to 50%, 75% and 100% of pages). The symptoms came and went away at about (but not exactly) the same time I tried that... this was the code that I used:

$(document).ready(function() {
  window.trackScrolling();
});

window.trackScrolling = function(){
  var waypoints = [0.75,1];
  waypoints.forEach(function(wp,i){
    var dh = $(document).height();
    var wh = $(window).height();
    var currentUrl = window.location.href.split('?')[0].replace(/\/?$/, '/'); // <-- could that f**k s**t up?
    waypoints[i] = new Waypoint({
      element: document.body,
      handler: function(dir){
        _paq.push(['trackEvent', 'Scroll', wp*100 + '%', currentUrl ]);
        this.destroy();
      },
      offset: '-' + ((dh*wp)-wh)
    });
  });
};

Maybe some URLs are sent URL encoded and some not. Try _paq.push(['trackEvent', 'Scroll', wp*100 + '%', decodeURIComponent(currentUrl) ]);

Btw there's also this tool for tracking scrolls down the page in piwik http://rodi.sk/misc/piwik-scroll-depth/

Cannot reproduce yet