Okay, I understand now. Previously I thought you mean the "Project ->
Clean" menu was greyed out or something, but what you mean is that Eclipse
won't automatically add a checkmark to what is, in you opinion, the obvious
choice for which project that should be cleaned.

   It looks like the behaviour of which checkbox is check depends on which
editor or project has focus. If you have several projects open, and you
click on them in the navigator, then select the "clean" menu, the most
recently clicked project will be checked.

   If you have several editors open, each one editing a file from a
different project, and you switch between those editors, then when you
choose "clean", it will automatically check the project of the file of the
editor you last clicked on.

   So imagine you have projects A, B and C, and you have editors open for
files from each (A.a, B.b and C.c). Click on project A, then click on editor
B.b. Notice that in the navigator view, project A is still selected (unless
you asked Eclipse to link the navigator to the editor). Now go to "clean".
It automatically checks project "B", because that's the editor you were
looking at, even thought project "A" was the one that was selected in the
navigator.

   To me, it sounds like this is "intended" behaviour, so I doubt there's a
way to turn this off. You migght be able to submit a RFE (Request For
Enhancement) to add in an option to change this behaviour, perhaps.

   - Oliver