I finally solved this problem on my boat last weekend (just in time for the winter - oh well.) It turns out when the previous owner had the batteries replaced the shop that did the work did not hook up the ground on the VSR. As a result, with the switch in position 1 - which is normal, it would never auto switch and charge the accessory battery. When I would switch it manually to 1 & 2, it was so discharged that it would put a huge drain on the system. All I had to do was pull the batteries, charge them properly, and then put them back in and hook the switch up correctly. Now everything works fine with proper switching, charging, and voltage.

I suspect your issue is either with the way your VSR is hooked up or with its functionality. Your symptoms are identical to mine when the accessory battery was drained and not charging.