From the owners manual, which you can download here: http://www.fourwinns.com/customer-servi ... nuals.aspx

"The use of one battery at a time is recommended. Position the battery selector switch to either the #1 or #2 position. Under normal conditions, avoid using the “BOTH” position. Use the “BOTH” position only when a single bat- tery is not capable of starting the engine. Four Winns recommends alternating between batteries during boating. Depending upon boating use, this may increase battery longevity. Use battery #1 for the first day of a cruise and switch to battery #2 on the second day."

Thanks for the link and if you look at page 238 of the manual you will see my battery selector. The verbiage in the manual doesn't actually relate to the panel itself. They talk about 1, 2 and Both positions, but my panel has Off, On and two spots you can turn the dial to for Emergency start only. I'm confused as hell on this one and maybe I'm missing something here.

Check out page 70 of the Horizon/Freedom manual:

"Battery Switch Operation with “Emergency Start
Only” Position

The battery selector switch with “Emergency Start” po-
sition is standard on certain models only. A description
of the various positions for the battery switch is as fol-
lows:

“OFF” - With the battery selector switches in the “OFF”
position and the “SHIPS SYSTEMS” circuit breaker in
the “OFF” position, all 12 volt power to the boat is shut
off except to the automatic bilge pumps, stereo and wind-
lass (if applicable). Always turn the battery selector
switch to the “OFF” position when the boat is unattend-
ed for an extended period.

NOTICE
Twelve volt power to the cabin panel is supplied
by the “SHIPS SYSTEMS” circuit breaker on
the battery selector panel. This must be turned
on to operate any 12 volt accessories on the
cabin panel. The bilge pumps and stereo re-
ceive power from the ships system battery and
remain on at all time regardless of battery selec-
tor or ship systems switch position.

NOTICE
DO NOT turn the battery selector switch to the
“OFF” position while its corresponding engine
is running. Alternator and wiring damage could
result.

“ON” - Turning the switch to position “ON” will use the
engine battery to power the engine and 12 volt engine
related equipment. The ships system battery will not
be used for any engine related equipment, but will power
all other 12V equipment on the boat (when “SHIP SYS-
TEM” circuit breaker is on). The isolator will allow the
alternator to fully charge the two batteries, but not al-
low the operator to drain down the engine start battery.
“ON” is the recommended switch position for normal
boat operation. This position allows maximum use of
12V equipment on the boat and leaves a full charge in
the engine battery(s) for starting.

“EMERGENCY START ONLY” - With the battery se-
lector switch in the “EMERGENCY START ONLY” po-
sition, the engine and ships systems battery are con-
nected in parallel. Both batteries will be used by the
engine and all 12 volt equipment. Both batteries will be
charged by the alternator through the isolator."

Can you post a photo? Do you have one or two batteries?

You may want to tracy the wires from the batteries to the switch. That to will tell you how it is wired and how/what the switches work.

Yeah may be what happens. Just hoping someone on here may be an expert with that setup. Thanks.