Two possibilities:
1. Exit SMACX, then paste the screenshot into your graphics program, or
2. Add the following line to the [Alpha Centauri] section of your Alpha Centauri.ini file:
Directdraw=0
Now you should be able to paste your screenshot even without exiting the game. Adding that line also will cause the game to run at your system's native resolution. However, the line doesn't work on some systems.