Any time you update your custom timer job class and deploy the assembly to the global assembly cache, you must restart all the timer services in the farm. If you don’t restart the timer service, it will run the old copy of your timer job class. Yes, the timer service caches the assemblies. Restarting the SharePoint timer service is the only way to refresh the assembly cache and force it to use your updated assembly. You can achieve that from the command line using the following commands:

net stop sptimerv3
net start sptimerv3

Yes! I have learned that the hard way!