Office 2016 and 2013 users who use run-a-script rules are discovering their scripts are currently disabled (as is Start Application), thanks to a security update. When the update is installed, any existing run-a-script and run application rules will be disabled.
To fix, you need to set the EnableUnsafeClientMailRules value in the registry.
One option is to convert the run-a-script to an ItemAdd macro. Depending on the conditions in your rule, converting it to an ItemAdd macro may be as simple as adding the application startup macro, renaming the script, and adding an If statement. For information on using ItemAdd macros, see How to use an ItemAdd Macro.