tomvdj: I noticed that when you change the ingame resolution to 480 * 640 instead of 600 * 800, the flickering / disappearing of the arrow cursor is gone... It does not change a lot to the game. game windows will be just full screen and the menu will be bugger (so will look a bit less "high res"). But I prefer this 480*640 view with a "stable" mouse cursor, to be honest.
Going through Overseer now, and I have a similar issue with flickering cursor. For me, if LockVideo in the Tex.ini file is set to zero, it flickers anywhere on the screen while in-game. If it's set to 1, it looks fine from the bottom of the screen to about where 480 pixels in height would be, but anything above that and the cursor begins to flicker. So it's a coin toss whether I play the game at 640x480 or live with flickering on the top 1/4th of the screen, but I'm going to keep looking into this and see if there isn't some fix.
Edit: Running 640x480 causes now half the screen to have a flickering cursor. Setting the resolution in dgVoodoo2 causes the mouse to appear on the entire screen, but rapidly flickers.
Edit 2: Using RivaTuner and capping the frame rate to 120 caused the flickering to be a much less frequent concern, and lets the game still run smoothly. Probably if I didn't have an integrated Intel GPU and had access to a graphics card app with vsync and frame capping options, it wouldn't have been this much trouble.