> Scid always loses my layout settings. It starts with a wrong window size,

To save the settings for docked windows, you have to
Options->Windows->SaveLayout->1

> the background of the game and move list is grey although I switched it to 
> white,

Yah - ScidvsPC's back ground colour options is not working properly ,
but will fix it this week.
it is not a great thing anyway, for various reasons.

Many window managers export their colour themes/settings to ScidvsPC.
In my KDE4 , this is
SystemSettings->ApplicationAppearance->Colours->Options->ApplyColorstoNonKDEApplications

>  I also saved the layout after I rearranged everything according to my needs, 
> but next time scid starts up, everything has gone.

Perhaps you have unchecked Options->Windows->AutoLoadFirstLayout.?
Otherwise, if it is not a permissions problem for
$HOME/.scidvspc/config/options.dat, i cant help

S.A.

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