All build except the last 10 builds for the current configuration are stopped. The branch is not taken into account. This would require us to add controls to select a branch for each configuration repository. This is something that we will consider in the future and I have added this task to our to-do list.
If this is happening then we would like to find out why. We use the promotion timeout feature on our own build server and it is working fine. This is why we asked if there were any errors listed on the Event Log page, and requested a diagnostics report, so we can work out the cause of the failure in your environment.