Yeah, there's something weird going on with the launcher. I have a 2560x 1440 screen too, and my settings keep on getting knocked back to the same numbers you have: 2048x 1152. Moreover more, the launcher ALSO overwrites any changes I make to SkyrimPrefs.ini - not only resolution settings but also completely unrelated changes. Very annoying.
For a while, there seemed to be nothing I could do to get the game to start at proper resolution - no matter what, I was getting a weird window.
I was able to get it up and going properly by EXITING the Enderal launcher, THEN changing the iSize W and iSize H values (to 2560 and 1440), THEN restarting the launcher, and activating the OneTweak setting in the Launcher. My resolution numbers (greyed out) are STILL at 2048x 1152, but the game does start in borderless window mode.
However, the launcher continues to overwrite changes I make to the .ini file. So far, the only way I've found to protect other changes to SkyrimPrefs.ini is to set the file to read-only - though, of course, that pretty much shuts down the settings function on the Enderal launcher.