I constantly have the same problem (hardy with compiz enabled) with java
applications such as intellij IDEA.

Name: s3ptms-proxy - [/home/jvb/javaprj/legacy-jntc/trunk/proxies/s3ptms] - 
[s3ptms-proxy] - .../pom.xml - IntelliJ IDEA (Diana) #8418
Icon Name: s3ptms-proxy - [/home/jvb/javaprj/legacy-jntc/trunk/proxies/s3ptms] 
- [s3ptms-proxy] - .../pom.xml - IntelliJ IDEA (Diana) #8418
Icons: set
On Workspace: 0 ("Desk 1")
On Screen: 0 (Window Manager: compiz)
Window Type: normal window
Geometry (x, y, width, height): 31, 0, 1649, 1025
Class Group: java-lang-Thread
XID: 69207831
PID: <unset>
Session ID: <unset>
State: maximized
Possible Actions: move, resize, shade, unshade, stick, unstick, maximize 
horizontally, unmaximize horizontally, maximize vertically, unmaximize 
vertically, change workspace, pin, unpin, minimize, unminimize, maximize, 
unmaximize, change fullscreen mode, close, make above, unmake above, make 
below, unmake below

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some windows do not appear in the window list
https://bugs.launchpad.net/bugs/144406
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