I don't know if this is only a Mac thing, or even just a Tiger thing, but I found with the search interface for v.12 that I could only enter 1 letter at a time, and each time the letter would highlight and type over, unless I typed a right arrow after each letter. And I couldn't input two words, because the space bar just wiped the window. Instead, I made the following shortcuts on my dock, pointing to the v.12 help files in their folder on my drive.
go into the folder and look for "toclist" and "idxlist". That will at least give you the Contents and index, with no self-erasing search window.
suggestion courtesy of luckbat. So if you are having trouble searching in the Java interface, you might try this instead. Running 10.4.3, Safari 2.02.