Im going to speculate a bit here as this is a bit of on issue of comparing 2 different systems yes they have similarities but they are different.
One factor that may cause the disparity is that the user when clicking the link too quickly exits the site and does not allow piwik to process the entire image capture of data. If the click to and exit off site is quick enough some of the piwik data capture is not given time to process.
To compare to google or omniture if you want to get more accurate click through rates then i recommend you use CID or UTM codes in the referring URLs so that you can begin to do campaign analysis.
One factor that may cause the disparity is that the user when clicking the link too quickly exits the site and does not allow piwik to process the entire image capture of data. If the click to and exit off site is quick enough some of the piwik data capture is not given time to process.
To compare to google or omniture if you want to get more accurate click through rates then i recommend you use CID or UTM codes in the referring URLs so that you can begin to do campaign analysis.