I am trying to play a modded K2 with the highest resolution the game offers. But when I try to play I keep getting the notification, that the game is not set to native resolution. I keep getting it when the intro plays and when I transition to a new area, like the beginning. My resolution is 1920x1080. How do I disable the notification and just be able to play the game. I am on Windows 10 if that helps.

The game has cutscenes and loading screens that are 640x480 with no option to upscale for larger resolutions, so if your monitor can't go that low, its probably why you are getting the error. You can try disabling cutscenes in the game's options, if only to confirm that is at fault.

If you use flawless widescreen, there is an option to upscale the movies to fullscreen.
You can also disable the pre-rendered movies (not the in-engine cut-scenes) by using the config tool in the game directory (this may fix some crashes).
Here is the guide for all things widescreen and mods:
http://deadlystream.com/forum/topic/3142-guide-xuuls-ultimate-guide-for-kotor-2/

I´ve experienced the same issue. For me, it helped to run game in XP/SP2 compatibility mode + "run as administrator". However, I was looking for the solution on the web and although it can help in some cases, this is definitely not the universal one... Good luck with that!

I run the game on Windows 10 with a 1920x1080 display, using Flawless Widescreen (all KOTOR2 options on), and have set the compatibility for the shortcut to WinXP SP3 (the latter primarily to ensure that the racing mini-game works properly without getting stuck on the roof). I have also configured the shortcut to run the game in fullscreen mode (with the "-fullscreen" option), so it doesn't start windowed.

I'm also running the latest TSLRCM, plus have incorporated lots of HD mods to enhance as much of the graphics as possible - but Flawless Widescreen + WinXP SP3 compatibility settings should do the trick regardless.

Oh I also needed to run the game as Administrator - but you should probably be prompted for that anyway.