There have been 2 instances now where the Script checkbox under "IIS > Sites > Site > Handler Mappings > Edit Feature Permissions" has become unchecked. What could possibly be causing this to occur? Haven't been able to find any information online about others experiencing this problem.
This could just be a coincidence but I just realized that this has happened twice now within a day or so of posting a full update to the folder which the site points to. Usually we upload a new folder of code, rename folders and the new folder takes the place of the old folder. The permission does not immediately uncheck, it is hours later. Is there any reasonable explanation why this might cause the script permission to disable automatically?