I seem to remember that in window mode when I had my desktop at 1024.
Are you window mode or full screen?
Whats your Desktop size set at? 

Should be able to set also in the user.setting in
C:\Users\myfist0\AppData\Local\Ironclad Games\Sins of a Solar Empire\Setting\
C:\Users\myfist0\Documents\My Games\Ironclad Games\Sins of a Solar Empire Rebellion\Setting\ ???

Open with notepad

VideoFullScreenWidth 1024
VideoFullScreenHeight 768
VideoWindowedWidth 1024
VideoWindowedHeight 768

Maybe this file is now read only?

EDIT: Been a while since I messed with that. My desktop is set to 1920x1080 and I play window mode. I can set in game to smaller with no effect, it stays same settings as desktop. If I go full screen mode, I can change with effect. Actually going from dev mod to reg mode rewrites the settings file so it starts at 1024x768 full screen every time in normal mode  . Dev stays window mod so I dont have to change that as its the same as my desktop even thought the setting file reads as above.

So, I just bought the game and the first thing I did was going to options and changing the settings. I had the same problem but I found a solution!

1. Go to: Documents\My Games\Ironclad Games\Sins of a Solar Empire Rebellion\Setting\rebellion.user.setting
2. Open it with Notepad
3. Find VideoAdapterOrdinal
4. Change the number after that to 1 (mine was 0)

That's what I did at least and it worked for me, maybe it's a different number for you, so keep trying

Hope that helps.

didnt work?  maybe can you just copy the file contents in so we can see the settings and compare?