I have a 1986 F250 6.9l 4x4. To start, I've had my truck parked since the ending of winter as problems are just seeping through the woodworks it seems. I originally parked it and left the 2 new batteries in (bad idea I know) but I was gonna tear into the issues in June. I took the batteries out and put them on the charger, one of them charges up to 12.8v but the other only charged to ~6v which indicates to me that something in the truck is sucking power when the whole truck is off. That's issue #1. #2 is when I was driving the truck the previous summer and beginning of winter the driver side power window would go down but going up you hear the motor spin but window wouldn't go up (indicates bad motor or track), and the passenger window would go down and up slowly which to me indicates another bad motor. #3 is the power locks on passenger door worked but drivers side only worked sometimes. This is where I'm baffled; I put the one battery in with 12.8v charge to work on the window motors and door controls and non of the controls worked at all not even a whir from the motors, so I started with the passenger door and replaced the window and lock controls and the window motor and still not a thing, no movement or sound and I was getting voltage to the controls. Need help where to start from this point, I thought I may need both batteries??

 

It's really important to note that "dual batteries" are basically a matched pair of cells, (electrically) in lieu of a single large, high ampere battery. They have to be charged and maintained in parallel for them to last or perform well. One for sure or both of your "cells" is junk at this point.

Most (retail) chargers aren't "sized" properly for a large battery as found in dual setups. A battery will self discharge especially in warm weather apart from any parasitic load the vehicle adds on top of that. Because of the expense of replacement and possible damage to charging systems or sensitive components it pays to keep them serviced and fully charged.

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If you charged each battery separately, and one isn't taking a full charge, that's just a plain bad battery. The batteries are in parallel, so if there were a parasitic load, it would have discharged both batteries. If the batteries are fairly new, and have a decent warranty, that bad battery should still be in the free replacement period.

 

The batteries are connected in parallel, but it wouldn't surprise me to find that one or the other is tapped for certain circuits, that would result in uneven discharge. Regardless tho, dead batts will be ruined after a period of time. Both should be replaced. Too, cables and connecting hardware, ground points, alternator connections are almost 30 years old, any uneven charging probably start with corrosion. The idea here is to prevent a continuing cycle of problems and expense in the future.

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I charged both batteries separately outside the truck using the same charger for both. Either way I'm gonna replace both batteries but before I did I wanted to use the mostly charged battery to test window and door controls with ignition turned to acc. I shouldn't need 2 brand new batteries just to test door controls and at least get a groan from the window motor, should I?

There are more electrical problems with the truck that I look to fix due to the previous owners but I'm just trying to fix one item at a time.

 

That's electrically impossible with the batteries connected in parallel.
Correct, you shouldn't need both batteries to run the accessories. After all, they're the same accessories as a gasser truck with only one battery. Ah, but there's the rub. One other difference - the glow plugs. It could be that when you turn the key to RUN to test the accessories, the GPs are cycling, and pulling the voltage down. So for any accessory tests, since you're not attempting to start the engine, disconnect the glow plug relay for the time being.

 

Provided both batteries actually *are* in parallel -- That is, that the wires on one are not so corroded as to not provide any real connection between the batteries.

One good battery will start one of these trucks in decent weather(i.e. not below freezing). If you have a marginal battery though...

 

The positive on the driver's side battery is connected only to the positive on the passenger side. I suppose if that crossover cable, or either battery ground cable, were severly damaged (and it would have to be REALLY severe damage), the truck would effectively run from just the one well-connected battery. But even a long slow discharge should not kill a brand new battery to a point where it will not take a charge past +6V. And the OP would have had serious starting issues back before he parked it, when both batteries were supposedly fresh.

But this inspires a question for the OP - when you were working with just the one good battery, attempting to test the accessories, in which position did you have it?

 

With only one battery available (that's been rode hard, put away wet) glow plugs kicking in - yeah even though charged, it might not be a good way to troubleshoot I'm thinkin. Just because it will charge up doesn't mean it's "good", a load or conductance test will tell the tale.

Remember you want to eliminate any unnecessary variables. Doesn't mean two "new" batteries, but would mean ideally two serviceable batteries, replacement cables, clean up the ground connections, etc

Substandard current, as well as substandard voltage, does all kinds of strange things and mimics component failure.

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Testing with just one battery I have the battery in the passenger side, the cables to parallel both batteries look good and grounds have been wire wheeled for connection. The ignition when testing is either tyrned back to the acc possition or the on possition. It shouldn't be cycling the gp as one of the previous owners put in a manual switch. (Gp's are another problem I'll deal with later though). Another thing I checked when trying all the controls is fuses, and they all look good.