I've seen this also.  As much as people want to make Windows and UNIX play 
nicely together, there are just somethings that don't translate between the 
systems.  The file system and file structure is one huge difference.

I would see similar issues when logging into our AIX master server using the 
Java interface versus using the native Windows GUI.  We ended up developing an 
internal policy that if you needed to restore a Windows file, use the Windows 
GUI and the Java GUI connecting to the AIX server for UNIX restores.  
Thankfully, 99% of the Windows restores were done by the Windows team so I did 
not have to constantly switch between the two interfaces.

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