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050125 custom, JDK 1.6.0. I have java/j2seproject open and I click on its root node in Files and search for the string "javadoc.additionalparam". At first I got a match in J2SEProjectProperties.java (correct) but none in build-impl.xsl (where it is also used). Later I got no matches at all, but later still I got the first behavior (no idea why). "Find in Projects" also claims no matches, though it finishes so quickly I think it didn't even look.
Occurences of "javadoc.additionalparam" are not found in .xsl files because .xsl files are skipped during search. It has already been reported as bug #52256 ("Find does not work on XSL nor XSD files in 4.0 RC2"). You also claim that you got an empty result at least twice (once when searching the root node, then when using the "Find in Projects" action). I was not able to reproduce this bug. Are you able to with the latest build?
I found that some of the nodes are not displayed even if they are not skipped. It is a new bug - I filed it as a bug #54085 ("Not all found nodes are displayed in the Search Results window"). So this bug is actually a compound of bugs #52256 and #54085.
I lowered priority of bug #54085 so I lower priority of this bug, too.
Both bugs covered by this umbrella bug are fixed. Marking this bug as FIXED.
See also bug #54436 ("Root node claims no nodes were found but there are some nodes displayed") which might have been partially caused by a patch for this bug. But it also discovered a threading problem which might have been causing symptomps like the one described in this bug.