One octave pedal board may be the cause of the back pain, if used incorrectly. It might arise from playing with the right foot in the bottom of the pedal board of such organ. This kind of instrument is mean to be played with the left foot most of the time. And of course not that kind of music with the independent pedal part like most of classical polyphonic organ music. Incidentally, the right foot usually is busy operating the swell pedal and pressing the toe studs where available.
Originally, the electronic organs with the short pedal board were intended either for playing classical transcriptions from popular works or the arrangements of tunes from pop music. In both cases, the texture is rather homophonic with the melody in one hand (usually in the right) and chordal accompaniment in another.
The pedal part in such music is mostly the bass voice which only supports the chords and serves as harmonic foundation. Very seldom it is required to play an independent melodic line in the pedal part of such arrangements. Therefore, one can easily use only the pitches of the available one octave to play the harmonic foundation with or without some rhythmical syncopation.
Contrary to such arrangements, in classical organ music the pedal part is very often independent. The organist is required to use the entire compass of the two-octave pedal board, often playing the higher notes up to treble F. Naturally, performance of most of organ music on electronic organs with one octave pedal board is quite challenging.
The solution for this problem is rather simple. The organist could try to extend the short pedal board by attaching a wooden board with similar dimensions as the pedal board. One can go even further and draw the rest of the notes on this wooden board. This way it is possible to pretend and imagine the full pedal board very easily (and avoid dangerous tension in the back).
Some organists try to compensate the short compass of the pedal board by lowering the pedal part in various places of the music score. This is a possible solution to the problem but is rather inconvenient and might cause some frustration. Instead, it is probably better to extend the pedals with a wooden board.
If you will continue playing pedals on your electronic organ, it is best if you avoid playing with the right foot on the extreme left side of the pedal board while practicing. This may mean adjusting the pedaling when necessary. In addition, use the idea of extending your pedals. Otherwise, you could try to get some practice time in churches that have organs with pedals of at least two octaves in compass in your area.
By the way, do you want to learn to play the King of Instruments - the pipe organ? If so, download my FREE video guide: "How to Master Any Organ Composition" in which I will show you my EXACT steps, techniques, and methods that I use to practice, learn and master any piece of organ music.