There is a caveat that is given for any Workflow Trigger that is setup in JIRA:

Caveats: Conditions, validators, and permissions will be ignored for automatic transitions but operate as usual for manual transitions.

For an Automatic Transition, according to the instructions, any Conditions,etc. set on Triggers will be ignored. This can sometimes be a problem, especially when a Condition is desired, since operations can occur (such as issue reopens), that are unwanted.