Could just be a total fluke. I know it's a bit drastic, but you could try a fresh install. Other than that, you might just have to work around it. You could save the file, do the node in a different version of Blender, then load it back into 2.49 and just ignore that it doesn't show up, trusting that it is there - if you haven't done that already. Blender is very good about files working on all versions of Blender.
BTW - I think the keyboard shortcut for a screenshot in Blender 2.56 is Ctrl-F3, I dunno where the subwindow screenshot went to though.