I have the same problem. Everytime I shutdown when I restart my font size changes have all been changed back. There might be a default setting in WB for using custom settings instead of the Blind settings. I'm willing to wait till the pros respond on this. Good question though.

For colorizing a skin, you have 2 choices:

1 - use the "Change skin color" link found (I believe, if memory serves for version 4.4) on the right side of the preview pane when looking at the "Skins" list in WindowBlinds configuration panel.

2 - use the SkinStudio program to edit the skin and save the changes if the "Change skin color" function in WindowBlinds configuration panel does not serve the purpose you need.

For fonts, you have similar choices:

1 - use the "User Overrides > Font Overrides section" to select a font. You can make the fonts larger by increment of 10% but not smaller. Make sure to click the "Apply Changes" link on the left side of the WindowBlinds configuration panel after making your choices.

2 - use the SkinStudio program to find and edit the fonts as needed. This option will also allow more advanced font selections (color, shadows, etc.).

The options listed above for the WindowBlinds configuration panel require the use of the full version of WindowBlinds. If you are running the shareware version, then many changes made will not hold after reboot.

I will leave the technical details of using SkinStudio to the real skinners.