Yosemite GM has significant bugs affecting the ability to add accessibility permissions for various applications, including Keyboard Maestro Engine, as well as engines for various other applications like TextExpander and Which.
Hopefully Apple will promptly resolve the problem as it is affecting a lot of people. In general, I believe you will be fine if you have already enabled accessibility permissions for Keyboard Maestro and the Keyboard Maestro Engine and then upgrade to Yosemite, but if you clean install Yosemite then it appears quite difficult to convince the system to enable accessibility permissions for Keyboard Maestro Engine.
Generally you can force the system to add Keyboard Maestro Engine with this sequence:
- Open the System Preferences ➤ Security & Privacy preferences.
- Switch to the Accessibility settings.
- In the Finder, control click on Keyboard Maestro.app, and choose Show Package Contents.
- Drill down into Contents / Resources and find the Keyboard Maestro Engine.app
- Switch back to System Preferences.
- Click the Lock icon in the bottom left and enter your admin password.
- Click the Plus (+) button to add an application.
- Drag the Keyboard Maestro Engine.app into the open dialog.
- Click Open.
Even if nothing appears in that last stage, it may still have worked. Launch Keyboard Maestro and see if the setting is actually enabled, and if not, try restarting.
The folks at Many Tricks have a detailed walk through, including a video, and the process is very similar for Keyboard Maestro, so if you’re having troubles folling the instructions, that might help.