To enable more debugging information in Bamboo (this list is from incoming Bamboo 5.7 but most (or even all) will also work in 5.6):
First thing to try if you can is to update both Stash and Bamboo to newest available versions. I know that Stash had one bug (events flood detection triggered to eagerly = events stopped being sent) and I think Bamboo had one fixed too. (I can't check which versions right now)
One more thing you can observe is - if problem is only with branches or also on master.
The way it supposed to work is - it does sort of ping between Bamboo and Stash. When Bamboo detects that remote events are not working it should fall back to polling. In Bamboo 5.7 there is a additional section (system configuration admin) showing connection with Stash status, but it's not released yet...
Plan B would be to switch to polling trigger until you can diagnose it better in 5.7.
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