Based on your post, I'm guessing you want to switch to both larger and smaller resolutions than 1280x1024? Last time I checked, Xorg will only let you use resolutions smaller than the resolution that you have set as the default. I'm not sure if that is the issue here, but it would explain why using xrandr seems to fix things.
When I had a CRT monitor, I used to boot X with 1600x1200 and switch to my preferred resolution with "xrandr -s 1280x960". I placed the xrandr command in xinitrc, but since you a using a login manager it will be a different place. Maybe find out what login manager you are using and read the documentation.
So yeah, I'm not sure if that is any help
You could login from the console and just use startx. Editing xinitrc is pretty straight forward.