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[ BUILD # : RC2 ] [ JDK VERSION : 1.4.2_xx ] Go to Tools->Options->Fonts & Colors->Annotations. Select Bookmark. Set the Background color to RGB(204, 255, 255). Click 'OK'. Open a file. Go to an empty line in a method. Type 'Ctrl-F2' to set a breakpoint. The background color should display baby blue, like the bookmarks icon. Now enter code which will cause an error (e.g. getTime();). You'll see the 'Show error' icon displayed in the left column and the code will have a red squiggly underline on it. The baby blue background color, however, will disappear. The bookmark works. I see other issues here as well. If you type 'Ctrl-F2' to set the bookmark again (you'll have to do it twice, once to undo the previous bookmark and again to set it again), the error icon and squiggly underline no longer display. However, the suggestions light bulb still displays.
Looks like if the error annotation that does the underlining would also set the background so that the bookmark's background does not show up. I remember that the new options did this for some time (i.e. setting background explicitly although it should stay non-opaque) but I hope this is no longer the case. Anyway IMHO we should first find out whether this happens or not.
The problem is still in a dev build. If you change the primary annotation by clicking the little arrow in the gutter the bookmarks icon and background will show up and surprisingly will get merged with the underline.
Still valid in latest build 6.0 I will add two additional symptoms. If you have two bookmarks on two following lines and delete the first line and undo it, then the second bookmark is set, but there's not colored background on that line. Another issue is that when you change bookmark background color in options and confirm it, nothing happens until you move your carret in editor.
moving opened issues from TM <= 6.1 to TM=Dev
Regarding the original problem this is the way the annotations currently work and we won't be able to redesign it for 7.0 very likely. We will resolve it later.
NetBeans.org Migration: changing resolution from LATER to WONTFIX