I've never seen this.
It sounds like like Maemo/Hildon/whatever challenges the claim of the ED window to be on top of everything else.

shot in the dark:
Does the flickering go away if you unmaximize the ED window by pressing Ctrl+Backspace and the return to it?

None that I know of.
Theoretically you should be able to create a virtual desktop within ED that is bigger than the N900's screen. I never tried that with xephyr and a touch screen, so I don't know if it actually works or if the result would be useable.

What should work is to move the window by selecting the "move" option from the window menu and then dragging the window to a position where you can reach the input field and button.
This will at least work once but might not work a second time if you have to move the window to a place where you can't reach the window menu again. In that case you migt want to have a look at wmctrl. It's a cli tool which (among other things) allows you to move windows, so you could call it from a terminal to move the brower window to the right position. In connection with xbindkeys you could even bind that window move to a keyboard shortcut.