I think it is all as it should beand point out some of the things that are hard to get folks to believe!
One of the first things to note is that battery charging is not a quick process,so connecting to an alternator rated for 125 amp or a converter rated at 50 amps will NOT change the amount of time it takes all that much for simple reasons. It takes TIME!
The rated output of any charging system is how much current that system can put out without danger of overheating, not what it DOES put out with any given cable and battery setup. What controls how much current a charge system can put into a battery is the voltage if we keep the resistance the same. Since we don't want to up the voltage enough to burn out things like lights that are on the battery system, we have to stay around 12-14 volts and since the resistance is still going into the same cables and batteries whether we use a 125 or 65 amp rated charger is not making much difference.
Current is the voltage divided by the resistance, so if the resistance stays the same and all we can vary is the voltage in a small range, we really can't shove much more current into the battery by using a higher rated charger once we are using a charger which DOES put out the maximum current the batttery can safely handle. If we can charge a battery at ten amps maz, there is nothing to be gained by using a charge systems that maxs at 125 versus 65.
But the time is not so much a factor of whther we are using generator to power the RVconverter or if we are using shore power to feed that same converter. Same converter does the same thing, no matter where it gets it's power!
But the timing can certainly fool us really easy whenn we look at the time it takes to get from one state of charge to another as that is not a straight line going from 50% to 75 % versus 75% to 100%.
Ohm's law states that the current through a conductor between two points is directly proportional to the voltage across the two points.
That needs some thought for a clear picture of why charging gets confused.
When we charge a battery that starts at 10 volts, using a charger outputting 14 volts, the difference at the start of the charging is 4 volts across the two points as mentioned above. If we plug those numbers into Ohm's Law we get current= 4 divided by the restance X. (I = 4/X)
But when the battery gets partly charged the voltage will have increased, so lets say it now reads 11 volts instead of 10? The difference between the two points, charge and battery will now only be 3 volts and that changes how much current flows!
I= 4/ X gets you more current that I=3/ X !!
And as the battery gets closer and closer to fully charged, the current drops and we can continue to see the reason for that drop if we set up more formulas to compare.
When we get into the voltage difference being 1, .5, or. 1 volts, the current continues to decrease dramatically! Plug in any theoretical number for resistance and the numbers may make more sense. I like 10 as an easy one to use!
The better charge systems will also drop off the rate of charge as the battery reaches full charge.
So your question was why did it appear that the convertor worked different when on generator than shore power?
I might also assume there was some difference in the amount of power being used in the RV at different times. That power comes out of the batteries and it may be things that we may miss. Weird things can sneak up like opening the frig, plugging in a cell phone, leaving the steps out so the light is burning, or some odd thing we don't spot???
For why it takes so long, I can only say it is the chemicals involved and it takes time to get them back in order. That is one of the big challenges and reasons for all the work being done on newer battery designs. Lithium works faster than lead and the even newer solid state batteries are making the lithium look "old school".
This is a site with chart info that I like for showing how long and slow lead acid batteries take and it comes out showing a good charge may take 9 hours or more!
The big point is that folks who are sure they charged their batteries in less than an hour are missing something or doing something the industry would really pay a lot to know about!
I'm betting on a bit of confusion involved!