After spending a day googling and finding partial solutions, such as "run in windowed mode" which also limits the game to 1280x1024. I figured i'd combine the fixes into something that produces the result desired, without the need for external apps messing with desktop res etc.

All you need to do is run the game with -d for windowed mode, and edit the registry resolution settings.

1. Right click your Total Annihilation shortcut and go to preferences, add -d to the end of the shortcut like so --> xxxxx\TotalA.exe" -d

This is what fixes the inverted colors and/or flickering black bars, obviously. But here's how to get it in a proper res you desire.

2. Click on your start menu and type "regedit" to open the registry editor, look for HKEY_CURRENT_USER\Software\Cavedog Entertainment\Total Annihilation
3. Edit the "DisplaymodeHeight" and "DisplaymodeWidth" settings, note that they are in hexadecimal, so look at the number in the brackets which will be your effective resolution.

In my personal example, i wanted to run at 1680x1050, but 1050 is impossible to get with hexadecimal values, 1049 being the closest. It makes little difference as the game still runs at 1-pixel less, barely noticeable. Especially considering a hidden task bar takes up 1 pixel anyway when hidden :)

I did end up setting the values at 400 (1024) and 690 (1680) respectively, as this gives a perfect resolution covering the entire screen except for the taskbar, and lets me see the bottom tooltips in TA without it being hidden below the taskbar. So while this isn't true fullscreen it is the best easiest and fastest solution i've come across.

Do note the resolution will only take effect when ingame, not in the menu.

Works perfectly for me - thanks!

Windows 7 randomizing my background caused the inversion of colors. Turned that off and TA played fine.

Uhh... Integer hexadecimal can express any value. 1050 is 41A

Thank you to OP for raising this issue, and thank you to xycury for mentioning the randomizing desktop causing it. that is also what was causing it for me, turning it off solved the issue.

Sadly running in windowed mode disables the cinematic.

For me the game would not run at all so it left me with little choice.

When I try the -d option, it runs in a window, but one without any borders or title bar, so I can't move it. I'm running Win7, 64-bit.

Yeah i'm afraid you'll have to set the resolution to perfectly match your desktop, then it'll hopefully be fully sized on top of your task bar and the rest so it appears as if it was full screen. I don't know any way to have it windowed with borders.

Any thoughts on how to deal with this on the mac?

You might try using PaultheTall's wrapper with the Windows version (his Mount & Blade Warband wrapper works great (or did until I installed a non-Mac Radeon 7950 in my Pro)). I'm downloading the Windows version of TA right now, but I'm going to install it in Parallels and figure that'll more or less work fine (since the Mac installer doesn't seem to work with ML).

What do you mean by that?

I had set my Windows background to change every 5 minutes, so when it did that, it completely hosed up TA with what was described here.

I haven't tested it in Windows 8 yet... but that's what I had to do to stop it from flickering and colors off.

Oh alright, I figured that is what you meant, I just wanted to make sure. Unfortunately, that did not work for me(AMD apu), but the TA Resolution thing did, or the fix mentioned at the beginning of this thread. That, and I have to put my font size back at normal(I use the larger setting because I sit at least 2.5ft away from my screen). But thanks anyway.

I can not tell you how thankfull I am!!

I had the flickering problem and this fixed it, but I didn't have to enter the registry.

Open the game in non-windowed mode

Go into the settings (single player > options > visuals) and change the resolution to what you want.

Now close the game and open in windowed mode, the menus will still be small resolution but when the game launches it will be your set resolution.