hi,
i have a 90 e-tec and when i fitted a second battery and isolator switch i experienced the same thing. mine does it some of the time but mainly with the second battery? i have asked brp and dealer and general opinion is that it has something to do with voltage drop. brp said to check battery terminals. my number 1 battery is 720 cca and my second battery is 600 cca (mainly used when anchoring but i do start motor with it to charge it up). my battery terminals are the cleanest you will ever see, tight and cables are connected with nylocks (not wing nuts). everything is perfect so now i have got used to it and do not worry at all.
cheers,
nick.