I had the same problem yesterday. The only way I could add an effect to a clip in the timeline was to click on the clip and then go to the drop down effects menu (as opposed to finding the effect in the effects pane/bin and dragging it over). But today, the problem has fixed itself.
Now I have a new mystery problem: I can’t click on a transition! I put 2 clips together in the timeline & normally I can click at the point where they touch and then choose a transition, like cross-dissolve. But today, even after re-starting FCP, nothing happens when I try to click at the transition point. I’ve been using Final Cut Pro for over a decade and this has never happened before.
FCP:6.0.6
System: Late 2009 Power Mac, 2 X 2.26 GHz Quad-core Intel Xeon, 12 GB memory