I am experiencing something similar, although the issue tracker doesn't seem to be the same issue.
I have 3 build configurations that use the same VCS root.
Two of the configurations are triggered by changes under source control, but exclude changes in all but one repository directory (different directory for each).
One of these configurations does not show pending changes or included changes in the change log, even though I have confirmed that build triggering is working as expected. The other two work as expected also, and the pending and included changes show up properly.
Why is this one configuration not working and what can I do?