When I double click on a CSS file (which CoffeeCup is the default editor for), the application launched and shows the file - no problems there. However, if I double click on another file, the file is opened in CoffeeCup, but the application does not become the active window. This is happening to me on Windows 7 - 64-bit. The same effect also happens if the CSS file is launched programatically.

Any thoughts on how to fix this?

When in beta a similar thing was happening when opening a browser through the validate HTML option in tools, if I remember correctly it was a sporadic windows OS thing, but will dig around a little. Are you using the editor in windows compatibility mode? Also try dropping a support ticket to the developers, you will get good help there also.