When the game boots to the menu the screen is black and keeps switching between my monitors, after about 2 minutes everytime by clicking on the other monitor and repeatedly clicking the application on the task bar I can get the menu to appear and the game runs smooth from there, but anytime I minimise the game the issue persists again and when I try turn it to windowed mode the screen goes black.

Does anyone know of any issues to resolve this? I read a different post with someone having a similar issue but couldn't find a solution that worked for me.

Try Windowed Mode with DXWnd
www.gog.com/forum/caesar_series/caesar_3_wont_launch/post5
www.reddit.com/r/impressionsgames/comments/5kwbzx/how_to_get_caesar_iii_to_run_in_windowed_mode_on/

Windowed mode via DXWnd allows you to bypass some rules:
- removes the window frame, which is so annoying for many in Windowed mode;
- you can drag the Game window to another monitor (the mouse will not stop working);
- bypass "noWindowed" bug in widescreen patches;
- bypass Color Rendering NOT 16bit for Windows7;
- (perhaps bypass Scaling is NOT 100% ;)