Please check "Mission Control" preferences
If you enable the "Displays Has separate Spaces" of OS X, Speedy may not always be visible. To solve the problem, access the preferences of Mission Control in the System Preferences (under Apple menu) and disable the "Displays Has separate Spaces" option, then restart the computer.
If the problem persist, please restore the app to factory defaults. Here is how:
1. Quit Speedy if it's running.
Note: whether Speedy should be not visible, search for "Activity Monitor" in Spotlight, open Activity Monitor app, go in the Memory pane, double click on the Speedy in the app list, then click on "Quit" button.
2. Hold the Option key and use the “Go” menu in the Finder to Show Library.
3. Delete this file if it is present:
~/Library/Preferences/com.apimac.SpeedyMac.plist
4. Launch the app in order to recreate from scratch the resources it needs by double clicking on its icon in the Finder.
If the problem persist, please check Accessibility preferences:
Check if the app has permission to use Accessibility services in OS X System Preferences:
System Preferences -> Security & Privacy -> Accessibility