Sometimes conflicts arise during Windows Startup. Such things as: ClipMate giving an error when it starts, no icon showing in system tray although the program is running, or an unwanted icon refusing to leave the taskbar.
If this seems to be happening, see if ClipMate runs ok if you start it manually. If it does, and the problems only exhibit themselves at windows startup, then you can delay ClipMate's startup by adding a 10-20 second "pause" to ClipMate's startup routine. Go to Config | User Preferences | Advanced, and set a 20-sec "startup delay". Of course, even if you start ClipMate manually, it will appear to do nothing for 20 seconds. But when you restart your system, this should let other tasks get out of the way before ClipMate initializes.
If ClipMate is causing an error at system startup and you need to prevent ClipMate from running, then hold down the SHIFT key as Windows starts. This will invoke ClipMate's Start/Recovery menu, which will let you abort.