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I noticed the same thing a couple of days ago. Definitely a bug. Seems like what is happening is that when it writes the VisualStyle registry key it isn't giving the full style name and since the name essentially doesn't exist it defaults to the Office 2003 color scheme.
You can open your registry editor and browse to:
Complete the data in the VisualStyle key. In my case, Microsoft Office 2007 Black was my preference so I needed to update the value from
Microsoft Office 2007 Bl to Microsoft Office 2007 Black, now I can open and close and my color scheme stays.
The options visual style can't save bug still exists in the new version of pads vx2.1