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ARandR problems: Bug or opderator?

I'm using Debian Testing on a Lenovo T510 Thinkpad whose screen is too small and is in the "short and wide" category.
I prefer my 17" diagonal external with a nominal 4:3 aspect ratio.

I am using ARandR Screen Layout Editor 0.1.9.
It reports:
  laptop as        1366 x 768  and normal orientation
  vga monitor as   1280 x 1024 and normal orientation

With those settings it _can_ and *FREQUENTLY* does display what I want.
Generally it chooses not to :/

I have two problems which I presume to be closely intertwined.

After a cold boot, if I open a text file with pluma it fills the laptop's short and wide screen.

*HOWEVER* it falls off the right side of the external monitor and occupies *ONLY* about 70% of its available height.
If I click-n-hold on the top of that pluma window while dragging down it:
  1. instantaneously shrinks as if "restore window" had been clicked.
  2. then be caused to properly fill the large vga screen by then
     a. continuing to drag it down so its bottom edge passes below
        the bottom of the laptop's screen
     b. clicking the "maximize" button causes it to properly fill the
        vga screen. As would then be expected does not fill the laptop's
        screen and extends below its bottom edge.

The second problem/symptom is designating the vga or laptop as "primary" does not change the above.

Some apps if shut down displaying in proper full screen on the vga screen will on next opening display that way. These include KeepNote, Zim Desktop Wiki, and Tomboy Notes.

For others the above rigamarole has to be followed. These include MATE Terminal, Caja, and Penguin Freecell.

When booting the MATE Desktop Environment always appears properly fulling the vga screen.