This is caused by the project (IIS Application) running in Application Pool with multiple worker processes (Maximum Worker Processes set to 5). Workflow does not handle this properly with multiple copies of project getting started and running at the same time. Multiple copies of project are visible in the 'Current Running Processes' tab in 'Workflow Explorer'. This, in turn, causes a timing issue where some of the timeout and escalation processing happens simultaneously by two or more of these project copies, effectively splitting the flow into two (or three). Dialog component/task timeout is one such place.
Make sure Application Pool for the problematic project has Maximum Worker Processes set to 1.