I had a similar symptoms before with my YBR. The engine light was flashing when the bike was hot and off. Difference being it wouldnt start until it cooled off. Yamaha mechanic checked it and it was a faulty lean angle sensor. He also said that when the engine light comes on only when the bike is off, it is not a danger to a motor. It needs to be checked out but the engine wont be damaged.
Dunno if this is true, its what he said ;)

P.S. Im going to buy The X5 in November but still thinking if I should get the carb or the EFI