Discrepancy in visits between Webtrends and Piwik

We are in the process of switching from Webtrends to Piwik, using log analytics, in a two server Windows farm. We have had both systems running in place for a few months. However, the number of visits have been significantly lower for Piwik than Webtrends. Unique visitors is slightly lower. We ran one month with static content and bots enabled and the numbers were still lower. Piwik and Webtrends both consider a visit activity inside 30 minutes. Any suggestions are appreciated.