There was a bug in earlier versions of Admin Tools which ended up removing the settings of the PHP File Change Scanner on update. I had posted the instructions in Admin Tools 2.5.1's release notes. Please allow me to copy them here:
As noted in the release notes of version 2.4.3, there have been some changes affecting Professional users upgrading from version 2.4.2 and 2.4.1. If you are one of those users please note that due to a bug in version 2.4.2 and 2.4.1 the PHP File Scanner's settings were not being saved correctly. As a result, trying to run a scan –even after upgrading to the latest version– might not work properly. If this happens please click on the blue Configure button in the PHP File Scanner page and set the following file types to scan (one on each line):
php
phps
php3
php5
inc
Make sure the minimum execution time is set to 1, maximum execution time set to 5 and runtime bias set to 75%. Then click on the Save & Close button. This will allow the PHP File Scanner to work correctly.
I hope that helps!
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!