An excellent example of this behavior is with the Job DSL. I'm having this issue, too.
Child jobs that implement a template are not updated if the template job is managed with DSL. Only when the template is opened in the web UI and saved (with no actual changes made) are the updates to all the child jobs triggered. It seems that the web UI save is performing some behavior to trigger the child jobs to go sync up, and that behavior is absent when the template job configuration is managed in any other manner than the web UI and hitting "Save". Managing job configurations by means other than the web UI is very common.
Thanks!
Apparently in 36749 changes didn't propagate at all. Now they do, but not after a manual update of the template.