It seems the the comment character ("#") is also used in some config option values as well as in some spawn names. I know this already causes problems when trying to define colors for grid lines and such where colors are defined per web style (eg: #FFFFFF for white). I imagine there could be problems elsewhere related to this.
So how are comments detected and seperated from the options? Quoting helps, but when the options are saved, seq doesn't seem to use quoting. Maybe fixing it so comments can only be on there own lines, changing the comment character, fixing the options that use the comment character as part of there operation, etc...
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The fact that there is no quotes around the color code never even occured to me until i saw your message 
