I may miss something, what do you mean by "pane settings" ?
the location for the locals, arguments, results, Current object and so on?
If yes, I checked again, and I have been using a setting different from the default one for the last 2 weeks without any trouble.

EiffelStudio remembers that I have 2 grids:
 - on the left: Stack information, Current object, and Dropped references
 - on the right: Arguments, Locals, and Result

And EiffelStudio always reload this settings.
Could you try again with 6.4.7.8332 for instance (available on ftp://beta:beta57@ftp.eiffel.com/)

And if this still fails can you give us more precise informations?
(platform, exact settings, ...)