My environment is a single WFE with two web applications. It had Collabion v126.96.36.199 before upgrading to v2 (Beta). After upgrading to v2 (Beta), charts on one web application seems to be working ok, while on the other it is not. The chart web parts built using v1.1.6 aren't working properly in one web application, after upgrading to v2 (Beta). I had to click on 'Edit Charts' and 'Finish' it to display the chart everytime I open the page. Also, I see a drastic difference in the configuration parameters between the problematic and properly working charts. Following are the screenshots.
Screenshot 1: (Properly working Web Part in Web Application 1)
Screenshot 2: (Problematic Web Part in Web Application 2)
Hope this helps you in troubleshooting this issue.