The isolator is doing exactly what it's designed to do, actually. But in reverse.
When you are using power from the AUX battery, the isolator disconnects the two batteries if/when the AUX battery falls below a specific voltage (cut out voltage for the UTV-SBI-18 is 12.9V, with a small tolerance). This is done to preserve your primary battery, responsible for starting and shifting, in the event you run your secondary battery down (e.g., lights, radio, etc.). Basically, it's making sure you have juice in the primary battery to start and get back to camp/home.
When charging, it's doing the reverse. It only connects the two batteries when the source battery has sufficient voltage (cut in voltage is 13.6v, with a small tolerance), then the other battery starts to charge.
Some say to put your charger on the side with the PRIMARY battery, so it gets charged first. I put it on the AUX battery.
My reasoning is that the AUX battery, which is used for all your fun stuff, is more likely to be drained lower than the primary, so it benefits you more to charge THAT battery first. Theoretically, the primary should already be in good shape because it's only being used for starting, shifting and the few OEM items on the bike, while the AUX (in my case) has a bunch of crap (all my aftermarket goodies) running off of it.
This would make even more sense if you only put the charger on the bike for very short periods of time -- if you only put the charger on the primary and it only reaches the cut in threshold shortly before you remove it, that AUX battery won't get a chance to charge up.
This is all anecdotal, of course. Realistically, as long as you're going to leave the charging source on long enough for both batteries to top off, then it doesn't really matter which side of the isolator you connect the charger to.