There were some problems using the newest Intuition.library 53.42 with the old ClickToFront 53.2, with that specific version of Intuition the commodity didn't work properly (Double click was broken) and so need an update
Now i don't know what AmiUpdate offer to you actually as new update, but you should find the latest version of both files:
Intuition.library 53.42
ClickToFront 53.9
With both of them updated the problem will be solved, atleast the double click issue (and the broken mouse pointer)
Now I'm confused too, since the issue I described is still here, using the versions mentioned above.
the "one-click" problem will be solved with the next update. with two-clicks it's fine.