You have to enable it for every new window, I believe. Since, you know, each new window opens with whatever the 'default' rotation settings are. (I'm fiddling with it now, and I'm not getting consistent rotation either, but I'm not actually connected to the internet, so maybe there's something like a "one per page loaded" rotation bug, or something. *Shrug*)

As for making something autorotate, you have to fake key presses - that's how shortcutd does it. (This is also why if you use the enable rotation shortcut in quick succession, you can see "Caps Lock On" come up. Because the OS sees two shift key presses closely together - where-as normally it simulates the ctrl-shift-r combination and then 'unpresses' the keys fast enough that the second press of shift isn't counted with the first... or something like that.)

Fake keyboard presses are part of the X window system's normal libraries, though I don't know of any way to run them from the command line. There's an xdotool program out there, but it's not ported from the N900. If you could do it from command line - dbus calls, or by porting xdotool, or some other method I don't know - then you can stick it in dbus scripts or something, and run it upon the opening of a MicroB window.