How to set default screen colours in putty/ssh
On the "Session" screen, click "Default Settings" and "Load". Then set up your Colors and other useful Options. Go back to the "Session" screen, click "Default Settings" once and then "Save".
All new connection windows will now look as expected.
The above instructions will only change colors for the default session. Most PuTTY users have saved sessions for each of the SSH accounts that they use regularly, and none of them are named "Default Settings".
To spare yourself the pain of having to set the colors every time you log in, load any of the saved sessions for which you wish to change the colors (click Load), but do not click Open. Click Window->Colours and set the colors, then click Session again, then click Save. Repeat for each of your saved sessions. Then when you open them, the colors will be what you have set them to be.