I suspect it's because the control profile is changed when it reverts to defaults. There are a number of different profiles you can choose from in the menu; one of them uses arrow keys and one uses ESDF, etc.

If the built-in keyboard layout workaround i added to PrBoom ends up working out without problems for people, i'm going to add it to UQM and make the joydev/accelemymote optional. The motives for that change of plans are

1. Knowing a way to do it that is fairly unobtrusive
2. Having no ETA still from Attila on the joydev package, and
3. Not really liking the accelerometer as a control for the game

UQM for Maemo 5 / N900 now has its own official thread and a new release that resolves (hopefully) all the issues i am aware of and have control over. Please take all discussion of the Fremantle/Maemo 5 version of UQM there. This thread will remain open for the discussion of earlier releases.

Thanks.
-Flandry