I have had issues like this one in the past with other programs. i would resize it, make it full screen and everything, but when i restarted the program it went back to what it was before i touched it..i fixed it by running the program in administrator by right clicking on the short cut and selecting "Run as Administrator"
I suggest you try this with LFS, launch LFS as administrator, resize your window and restart LFS, run it normally and see if it saved the size correctly