I have had exactly that on numerous trips to the Alps on my 2008 ST1300 Pan European - it can run really badly after a significant change in altitude. Switching off and back on sorts it out. I looked into this a few years ago and came upon an explanation that fits, but I have no evidence if it is correct.

I was told that when the bike is first switched on the ECU takes a base line pressure reading and selects the best fuelling map based on that pressure measurement. However, the particular map selected can only accomodate a limited range of pressure changes either way. In 'normal' use (the UK for me) the altitude changes I see are fairly insignificant and I never have an issue. When I go to the Alps however, I can change altitude by many thousands of feet very quickly without stopping the engine. Eventually it will start to run badly. Shutting off the bike and then re-starting allows the ECU to take a new base line pressure reading and select a different fuelling map. All is then well again. I have really only noticed the problem when descending, which is when it would get much more air at the lower altitudes and therefore be running weaker on a 'high altitude' fuel map. Can't say I have noticed any issues going up the hills, but I suppose it could run rich?

Now, this might all be a load of rubbish, but it sounds plausible and it fits the symptoms.

Anyone else had a similar experience? Any fuel injection gurus out there care to comment?