when i try to set nestopia to 1280x1024 on my desktop it looks like it has a black border around the game area, why ?
If you mean it's letterboxed, that'd be normal. 1280x1024 is a 5:4 resolution, whereas the NES aspect is 4:3.
It's possible he's running it on a 4:3 monitor though, every 4:3 CRT I've has since 1999 has been able to run at that odd resolution (1280x960 is 'true' 4:3). But if it is a 4:3 monitor, then Nestopia should really be filling the screen to keep the correct aspect ratio.
If you're running a CRT at 1280x1024 you're going to have aspect ratio problems with a lot more applications than Nestopia.