Windows X server problems

We have developed a Java application which is run under HP-UX with the gui (potentially) being exported to a Windows PC.
We have come across a number of intermittent problems with this, some of which we have been able to eradicate by moving to a different X-server (from Reflection-X to Exceed).
One problem that we have seen is Java windows appearing without frames, and sometimes placed in the top left-hand side of the screen. The move from Reflection-X to Exceed appears to have resolved this.
Another problem (which appears under either Reflection-X or Exceed) is that with multiple X Windows minimized in the task bar (i.e. from unrelated applications), launching a Java window frequently causes all the other X Windows to be restored from the task bar.
Has anyone else seen these problems, or know what the cause is ?

Guest access is enabled for SMB. I'm able to connect with windows client to PDC, created folder are stored on the server. But the profile seems to be loaded with its default settings.
NTUSER.dat and NTUSER.ini have different file permissions. Tried to propagate permissions, but that didn't help.
It would help to get informations about proper permissions for the "Profiles" Folder and the Windows Folders.

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