Start up !PackMan, and have it update, then upgrade. Reboot, that'll make it save settings.
Also, the icon in the icon bar for changing video modes (the display manager) is for temporary changes. You want to run !Configure, then Screen. I'd pick the Generic monitor, then pick the display mode that matches, and set it there.
Oh, and the icon at the far right of the icon bar (the RPi logo icon, on the RPi builds - it's an Archimedes or Acorn logo on Acorn's builds, a cube (for RISC OS 4.0x) or cog (for later versions) on ROL's builds, the Iyonix logo on Iyonix builds, and looks like it's a cog on BeagleBoard builds) is called the task manager. (If you select-click it, you get a task manager.)