You can control the colours from the "Connection Options" tab prior to connecting to the PSM system, unticking "Use Default Connection Options" and select the colours:
You can select the following:
Putty:Background: Black, Green, Blue, White
Putty:Foreground: Grey, Black, White
These settings will persist the setting will persist for this user every time they connect with this account to a session,
You can also change the colours of the current windows from within a PSM session.
After the PSM Session has started;
- Click ctrl+right-click on the Putty console window
- Select "Change Settings",
- Then go to "Windows | Colours" and it is possible to enter the colors for this session.