I have the same problem. I've found that actually becoming active (i.e. clicking on the break window that is in the "stuck" state) will usually restore normal operation.

Some mice, especially when placed on some surfaces, seem to generate continuous movement of a few pixels, enough to make workrave think you are still busy. Recent development snapshots have a "mouse sensitivity" field in the "Monitoring" tab, allowing you to tell workrave how small (or large) a movement it should ignore.

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