Rubenb - I only ever use the keyboard shortcut. The problem doesn't seem to appear on double-clicks. The error message has popped up both when running a single clip, and when running instances of the clipper in multiple tabs.
Same issue. Clipper works properly - opens, files, tags, and clips pages. Then serves the "<page> says: The Clipper couldn't start on this page. ..." dialog. Every time. OS X, Chrome v 52.0.2704.106 (64-bit), Web Clipper 6.9. Screenshot of successful clip with error dialog attached.