Having in the activation command/startFlow workflow mappings for certain paths work only once.
I configured two special flows for two sites.
On the very first activation, the spacial flow is picked up, but after the first activation never again.
Only a restart of the server makes, that the right special workflow is used again, but only for the first time again.

I added as a zip the flows, the configuration and all the users and roles.
Like this it should be easy to reproduce the problem.
I'm quite sure, its not a configuration error I did, but a bug.