it could be the fuelling or one of the sensors is slightly out?? sitting for some time could get it hot enough to "move" to another fuel map or slightly alter the parameters etc.???
Don't think it'd get hot enough to cut the fan in in 5 minutes, but the loading that puts on when it kicks in could result in a similar effect.
If it's not causing you any problems, and above all is OK whilst riding, then I wouldn't worry too much.............unless it's really bugging you
