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I start with a file selected in the navigator. I then do a search using the Search/file... menu item. The search dialog correctly gives me the option of setting the scope to "enclosing projects". Once this search completes I realize that I selected the wrong options (e.g. wrong file types, wrong search string) so try to repeat it. When I re-open the dialog box the "enclosing projects" option is grayed out. To re-enable it I have to select a file in the navigator before opening the dialog. While this is not a serious problem it is annoying. It seems to apply to all multi-file searches (e.g. Java and C searches) not just Search Files.
The scope is initialized with the selection. Bug 304641 would fix your scenario. *** This bug has been marked as a duplicate of bug 304641 ***