Goes GA track users that do not have javascript enabled (eg Mozilla desktop using NoScript, or mobile browsers)?
If you used Piwik API or image to track visitors maybe the visitor counts would increase?
FWIW, i use Site Meter on my sites and while i haven’t done any detailed matching, i did do a side by side comparison of Piwik visitors vs Site Meter visitors, and the ones that were missing were ‘javascript disabled’ in Site Meter which didn’t register on Piwik (i don’t use API or image tracking).