modal dialog takes a very long time to show up in a java application with gnome and nautilus

Binary package hint: nautilus

When opening a modal dialog from a java application in a gnome desktop that uses nautilus, nautilus collects all the java app windows into a single icon/entry in the gnome toolbar. When the dialog is dismissed, the gnome toolbar shows again a single icon/entry for each window of the java app.

The removal of window entries in the gnome toolbar repaints the toolbar each time (and I can see it removing the entries one by one) and can take from under a second to 10 seconds or more when having hundreds of windows open.

The archetypical java app with hundreds of windows is ImageJ, a public-domain application for scientific image processing of widespread use.

If I understood it correctly, the behaviour of the gnome desktop, that of collecting all windows into one when there is a modal dialog showing, is to prevent the selection/manipulation of other windows of the same app.

It would be ideal if:
 - the gnome toolbar did a single repaint, potentially eliminating all the lag without compromising the functionality.
 - the gnome toolbar just marked each window entry as inactive instead of removing it.

The current delay seriously disrupts usability.

ProblemType: Bug
Architecture: amd64
Date: Sun Nov 8 13:43:29 2009
DistroRelease: Ubuntu 9.10
NonfreeKernelModules: wl nvidia
Package: nautilus 1:2.28.1-0ubuntu1
ProcEnviron:
 LANG=en_US.UTF-8
 SHELL=/bin/bash
ProcVersionSignature: Ubuntu 2.6.31-14.48-generic
SourcePackage: nautilus
Uname: Linux 2.6.31-14-generic x86_64

Steps to reproduce:
1. Ensure that the test machine has a Java JRE v1.4 or higher installed by typing java -version in a command line; if this is not the case, install a JRE
2. Download ImageJ as a sample Java application (platform independent version): http://rsbweb.nih.gov/ij/download.html
3. Unzip the zip file
4. Start ImageJ by running the "run" script
5. Select File -> Open Samples and open as many samples as possible to create a large number of windows
6. Select Process -> Image Calculator to open a modal dialog
=> All window icons in the Gnome panel that contains the window list applet are coalesced into one, one after the other
7. Click Cancel to go back to the application

Actual behaviour:
- in step #6, icons for the ImageJ application in the Gnome panel are removed one after the other, until only one remain, taking a long time if there are a lot of windows open
- in step #7, icons are not restored and only one remains, even though the modal dialog is now closed; if steps #6 and #7 are repeated, you can get to a situation where all window list icons in the panel for the ImageJ application have disappeared

Expected behaviour:
- in step #6, window list icons in the panel should all be coalesced in one go rather than one after the other, or should not be coalesced at all but rather marked inactive in some way
- in step #7, window list icons should be restored to what they were previously