Two things to make ClickMouse work reliably:

-- Raise ClickMouse Delays on Settings Panel.

-- Usually you get better performance if the spot that you're clicking in background windows is visible (not covered by other windows). Sometimes (depending on PC speed and number of WoWs) you need to do this, other times you can get away with not doing it.

Also, make sure you're using the current build of HotkeyNet because ClickMouse's peformance increased in a fairly recent build.