If the battery charger is working as you state, then you should not be having these kinds of problems. First check the fuses on the output of the battery charger. If its like my 03 was there is one fuse for each battery. They are in a fuse holder behind the battery switch. You have to take the screws out of the panel and GENLTY pull it out enough to get to them.
Then I would take a voltmeter, 1 battery at a time, hook to the positive of the battery you are checking and to ground of that battery too. With the charger off, note the battery voltage, fully charged will be around 12.3 or so, give or take a few tenths. Now turn the battery charger on, the voltage should immediately go up to 13.2 - 13.5. Do the same thing to the other battery. If the voltage doesn't come up the charger is not charging the batteries.
Really this should be fairly straight forward to figure out. Start with the easy stuff and work to the hardest and most expensive.
Good Luck.
_________________
Jeff
'14 Cruisers 380 Express "Simon Sez"
Merc 8.2 Mag MPI 380
DTS B3X, (x2) Axius Premier
(SOLD)
'08 V318
Merc 350 Mag MPI 300
DTS Seacore, B3 (x2)
