Note: With ClipMate 7, this message will not appear - it will simply disable the hotkey.
When starting ClipMate, do you receive a message about the Ctrl+Alt+F11 and/or Ctrl+Alt+F12 hotkeys? If so, then you probably have an Intel Video Driver, and it has this key already assigned. If you press that key, you'll probably see something about your video preferences. The problem arises when ClipMate tries to reserve those keys for its screen capture. (ClipMate is one of the few programs that even bothers to check for such a conflict, other companies just assume that your bought your computer just to run THEIR software, and couldn't care less about anything else.)
So you need to relieve the conflict. Just re-assign these functions with ClipMate's Hotkey dialog, found under the Config Menu - then User Preferences - then the "Hotkey" tab.
With your mouse, place the cursor into the "hotkey" setting for the offending hotkey setting. Now PRESS (don't type) a key sequence. Let's say you want to re-assign the region screen capture to Ctrl+Shift+F12. Just press and hold the Ctrl key, the Shift key, and F12 at the same time, and the hotkey control (the little box) should indicate the new hotkey sequence. Or, if you want to just skip it, press the Backspace key to clear the hotkey to "none".
You need to press "test" to ensure that there are no (new) conflicts. Now you should be ok, and the error shouldn't come up again.
Note: If you receive more than 2 hotkey warnings, then you may indeed, be running ClipMate more than one time. For ClipMate 6, you should NOT have an icon to ClipMate in your startup folder - it uses a registry setting instead. Also, it's best to leave ClipMate running all the time - if you see its icon down near your system tray clock, just click on that icon to bring it up, or press Ctrl+Alt+C. Don't run the program again by clicking on the icon on your desktop or start menu.