Duck,
I had the same problem until I finally figured it out.
On the occasions it wouldn't disarm I would bring the fob very close to the lower right side of the fuel tank (almost touching it) and it would disarm almost immediately.
I guess that this method depends on where one's alarm is located/fitted.
I discovered this by trial and error (after hours of being stranded ... the first and only time).
I put this irregularity down to dense humidity (atmospheric) affecting the infra-red sensor (at least these are the conditions I noticed on the occasions this problem presented itself).
A simple test will indicate if it works for you too.
I hope this helps.
