Because of poor engine performance occuring when changing to a higher or lower altitude while cruising at a relatively steady speed (more noticeable when altitude changes 3000 feet or more)
Yamaha is currently sending notification letters (M2007-016) out to owners of 2006 and 2007 Yamaha FJR1300's, in this letter they let you know they are replacing the ECU's because of Altitude Surge. Not every FJR built within this time frame is affected, only various models with certain Vin Numbers are getting the ECU's. Yamaha has already started mailing this notification out as of October 16, 2007, inside of it you will be able to see if your bike is one that has been named as needing ECU replacement.

As far as warranty goes it does not matter if the bike is under warranty or not, all FJR's that require the new ECU will have them replaced at no cost to the owner. Yamaha is building the alternate ECU's for this fix as quickly as possible, but they will not be able to get parts for all customers at once. Dealers are asked to give modification priority to customers who are likely to use their FJR1300 in areas with significant altitude changes.