A.7.6 When I run full-colour applications, I see areas of black space where colour ought to be, or vice versa.

You almost certainly need to change the ‘Use background colour to erase screen’ setting in the Terminal panel. If there is too much black space (the commoner situation), you should enable it, while if there is too much colour, you should disable it. (See section 4.3.5.)

In old versions of PuTTY, this was disabled by default, and would not take effect until you reset the terminal (see question A.7.7). Since 0.54, it is enabled by default, and changes take effect immediately.