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Description of problem: Being able to set windows as transparent offers some interesting options, but sadly, when you set the transparency of a window, the state isn't remembered the next time you open it. For example, the Send and Receive Mail dialog in Evolution which come up each time it's opened as solid, regardless of the transparency level set the last time it was used. Transparency should be like size (and location) which is remembered when the window closes and then reused when opened (although sadly location seems to be a bit of a black art). Version-Release number of selected component (if applicable): compiz-0.0.13-0.32.20060817git.fc6
Try Devil's Pie which can remember and set transparency of windows among other thinges. http://live.gnome.org/DevilsPie
When an application remembers the size and position of it's window, it's something the application implements. Either using the session protocol or in gconf or similar. In other words, it's something the application needs to support. I would look into DevilsPie as suggested in comment #1.