Conflict with Chartboot

The plugin is really great! Unfortunately I now found that it clashes with the Chartboot plugin. Not always but sometimes. In these cases the entire post is not shown!
I have read in the documentation that it is possible to tell this plugin to not work for an entire post (<!--no-markdown-->). Is something similar also possible for the section of the Chartboot Code? Or is there some other solution to this problem?
Max

http://wordpress.org/extend/plugins/markdown-on-save-improved/