Charging 4 batteries

Not really. Normal operational charging via the alternator is a compromise.
Your best option is to hook up a trickle charger, maybe a 2 amp, no more than 10 amp. Probably one of the newer smart chargers.
Do this on your days off / home time. Other guys have reported that instead of getting 2 or 3 years out of their batteries, they can get 5 years life just by letting them slow charge over the weekend. It helps to balance things out.

 

No. Most vehicles, heavy truck or car are designed for 12v, the starter, everything connected to the electrical system. With 12v batteries in parallel the voltage stays the same, 12v. Two 12v in series would be 24v which is a problem if a system is not designed for that. While the voltage stays the same in parallel the amps of each battery adds together.
Are you having any issues that you want to "balance out charging"? Things are designed a way for reasons as explained above.

 

Are the batteries the same brand and same capacity as in CCA and Ah ? Have you disconnected the batteries and tested each one either with a load or capacitance type tester? Are all the connections clean and tight? Clean not as in look clean but removing the cables and cleaning the posts and cable. I have seen vehicles not start without any visible corrosion, just gray looking, and cleaning solved the problem. Check the resistance on each cable. There is also this thing called surface charge you may need to get rid of by letting the truck sit for several hours or turning on the lights for several minutes. Then test.

 

Think you are making a big deal out of nothing. But here's a video.
Bing Videos

 

If you are measuring voltage drop across the batteries you have a connection issues or increased resistance from battery to battery. Either inside the jump cables or at the eyelet connection to the battery post itself.

With everything clean and tight the the voltage should measure the same and the connection of the charge point at the bank does not matter.

 

Got the green goop up inside of cables ?
When was the last time they were changed ?

 

As said above, if the voltage has dropped from the first battery to the last then you've most likely got poor connections or rotted cables.

 

I do this with the batteries in my personal vehicles. Twice a year I take them out, top off each cell with distilled water, and then put it on the trickle charger. I do the same thing with a brand new battery before I ever install it for the first time. And once they're more than 2 years old, after they're fully charged I use the full-size charger's recondition (desulfation) mode for 24 hours.

Most of my batteries last 1-3 years beyond the end of the warranty.