Not a BMW but I had a similar issue with an Audi A4, both key fobs were acting as if the batteries were going flat ,went to a local car shop and they checked if the fobs were emitting a signal showing the batteries were okay and they were (new ones) .
Despite this fobs would not reintroduce themselves to the cars ECU and although they would start the car they would not activate any of the vehicles remote functions (tried three or four methods as outlined both on owners forums and by dealer mechanics and none worked.
Main dealer said I needed two new keys at £140 a pop, in the end spoke to a company who supply aftermarket keys and they said if i could get access to VCDS software (the equivalent of GS911 in BMW bikes) I could easily sort it .
I have VCDS and recoded both keys using VCDS Adaption codes and in less than 5 minutes had two fully functioning remote key fobs.
It is possible that your fob may not be faulty it is just that its signal is not being read or received correctly by the bikes ECU, worth looking into.
made his piss boil i’ll tell you 
“Well do you feel lucky? Do you?”
