350 fourtrax electronic shift problems

Hi. Can someone help me here. I have a honda 350 fourtrax ES 2005 and the electronic shift has all but stopped in both directions. Once in about 50 times it will move the gear selector and then nothing at all. There was recently a flat battery on the bike and it was started manually with the pull start until the new battery was installed. I have read some previous threads and it suggested that the new battery was not powerful enough, but I checked that with another battery and it is strong enough, also, I have tried to access the fault codes but there is no fault code coming up at all. everything else is working fine and the bike can be manually engaged by the auxillary arm that came with the bike when it was new.
Thanks for your help