I've noticed this issue several times when using Enhance's Move Server feature.
After moving a website to another server, custom PHP.ini settings and cron jobs remain visible in the Enhance control panel, but they are not actually applied or running on the destination server.
To fix this, I have to manually delete and recreate the affected PHP settings and cron jobs. Simply having them listed in the control panel isn't enough.
Has anyone else experienced this? It seems that Move Server transfers the configuration entries but doesn't correctly apply them on the destination server.