Any ideas what the problem could be? Batteries not charging properly

1. Measure the specific gravity (SG) of your batteries with a good hydrometer. They may have been destroyed by undercharging.
2. If this is a twelve volt system, you have four sets of batteries in parallel. This can easily lead to imbalance in the work that the batteries are doing and cascading failure.
3. If you can measure the expected short-circuit current from your panels at the leads which you disconnect between the panels and the CC, but little or no current from the panels into the batteries when you bypass the CC, then your batteries are toast The voltage from the panels is not a good indicator of their health or the adequacy of the wiring. You need to measure the current. If you are not absolutely sure how to do that safely, ask some more questions before you try. A clamp type AC/DC ammeter (cheap one from Sears for ~$50) is the best tool for this purpose.

What kind of CC are you using (is it PWM or MPPT) and how are your panels wired? (Series or parallel? Vmp and Imp specs? etc.)

Let me make sure I understand crystal clear.

You have a 1000 watt panel system, operating on a 12 volt battery, with a 40 amp MPPT controller? Is that accurate?

Is that charge controller MPPT or PWM?
What Amp Hour rating are those 6 volt batteries?

Re:

Okay. Going to try to answer both posts in one. First yes, 1000 watt system, (5) 200 watt panels in parallel, hooked to a PWM CC 40 amps. It is a 12 volt system. (I have eight 6-volt batteries in series and parallel.) The batteries are 225 amp hours. I really don't believe they are toast because they still read about 6.19 - 6.37 individually depending the time of day, and if I read as 12 volt, I get 12.79 or there about. So I know they are staying at a good charge. It's like they are getting continuous trickle charge. And they all are exactly the same. No weak ones. I don't have an hydrometer though I have been meaning to purchase one. The highest they got today is 13.20 and have always been at 14.24 by 1 pm.

Now, I am going to put all new cables on the batteries although at this point I doubt it'll make much difference. So, my next thought would be to take the solar panels apart. Read each on individually for output and redo that whole wiring in case something there is not working. I am at a loss here. Never had this happen and I have set up several battery bank systems.

Here is the odd thing. I have tried to eliminate bad battery cable wires by hooking up the panels to two 6 volts at a time. Then put my panels on it just to quickly see if there is any change. If I have the nuts on the pos and neg terminals tightened down the batteries read 14.25 or so. If I loosen the nuts up slightly, the charge shoots right up to almost 15.00. Then if I tighten them up again, it goes back to 14. 25 or so. The input coming in to those two batteries should shoot it way up, whether the nuts are tightened or not, but it doesn't. The output on my 1000 watt system panels today is 32.5 which is what it always has been. It seems that if I had a bad panel it would be lower. ?? I admit I am still a bit green on solar but as I said I have set up other systems and never had this happen.

So tell me, what would you do exactly next, in "layman's" terms. What's a few more gray hairs anyway. :/

OK here is the shocking news for you. You do not have a 1000 watt system, not even remotely close. At the every best you only have a 650 watt system. You heard me right, 650 watts at very best. I seriously doubt you even have that much because you said you have 200 watt panels, and I do not know of anyone who makes a 200 watt battery panel. I suspect you have grid tied panels and if that is the case you are down to 500 watts or less.

The first thing to do is get rid of the POS Charge Controller you have and get good quality 80 amp MPPT charge controller like a Midnite Solar Classic 150. Just by doing that and reconfigure your panels all in series will get you back to a 1000 watt system. Your PWM controller is robbing you blind. If you really have 200 watt battery panels each panel Voc = 18 volts and more importantly the Imp = 11 amps. Do some simple math 5 panels in parallel should be 55 amps and you only have a 40 amp POS PWM controller. That means on the output you have 40 amps x 12 volts = 480 watts. You screwed yourself big time. Move up to a 80 amp MPPT charge controller and the output is 80+ amps x 12 volts = 1000 watts. Please do not tell us you cannot afford a 80 Amp MPPT charge controller because you cannot afford not to.

Lastly you made a huge mistake going with a 12 volt system, and using parallel batteries. You should be using either a 24 minimum or a 48 volt system. What has likely happened is you are now usin gmore power than you can generate, or that 1-string of batteries that has been doing all the work all this time is now weak and dragging down the other the 3 other parallel strings you have.