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The Windows installer is supposed to come with the "Linux" color scheme pre-selected, which is more readable on a dark background.

It looks like there is a bug in the installer. The file you found .sage\profile_default\ is the right file, but it's in the wrong location. It should be under .sage\ipython-5.0.0\profile_default\

Incidentally Sage 8.8 for Windows was just released yesterday, and I confirmed that it has the same bug. I am working on creating a new release now, but in the meantime you can move the file I mentioned to the correct location and play around with your color scheme there. Some of the available default color schemes for the IPython terminal interface are given at:

It's worth noting also that dealing with colors in the console can be tricky. Most colors schemes won't change your background, for example, and are designed for either a dark background or a light background in mind. It's also tricky because the way colors work is that the application outputs specific color codes to the terminal, and it's up to the terminal program to decide how to interpret those colors.

Sage for Windows (which is based on Cygwin), includes the MinTTY terminal, a terminal emulator for Cygwin. You can change the color settings by right-clicking on the window's title bar, and selection Options. From there you can change things such as your background color.