I just purchased 3 100ah LiFePO4 Ampere Time batteries.
I have a MinnKota MK 4400 onboard charger, which according to the manufactor, .is compatable with Lithium LiFepO4 batteries.
Plugged the charger in for about 12 hrs. One of the indicators was blinking green (Charged), the other two indicators to the new batteries was solid yellow (charging).
Checked voltage at trolling motor, 40 volts.
Took boat out to test them, and the TM (Ulterra) worked great. Only fished for about 4.5 hrs
Came home, plugged charger in, next morning the indicator lights are blinking red.
I disconnected the jumper wires for a 36v series, plugged charger in and lights are yellow after a full day.
While they were charging I sent an email to Ampere Time asking about charging a 36 volt series system with my charger.
They said that I needed to disconnect jumper wires before charging. (Pain in the BUTT!)
My battery voltage is now 14.1; 13.8; 13.7 on the batteries. (Lights still yellow)
I know after reading the manual, that I need to balance the batteries by connecting them in parallel for 12-24 hrs, but this should have no bearing on charging them as you are supposed to charge before balancing
I tested voltage after charger had been unplugged for over an hour
According to the User guide I got with the batteries, 100% capacity of the batteries is 13.5 volts

Any help or suggestions is greatly appreciated!!!

I have the mk440pc, if yours is not the pc (precision charger) it may not charge them right.

mine works great on 3/50ah and one 125ah, I put it on a timer for 3 hrs a day and so far they are at 100% overnight.

mine are also bluetooth which is great, I can get a lot of info on battery condition/charge just by opening the app on the phone.

I have the ionic brand.

Can you please clarify which model charger you have. I'm unaware of a MK 4400. There is a MK440D, MK440PC and MK440PCL.

I have the MK 440D
I spoke with the tech at Minn Kota, Steve and he said my charger was not sufficient. That I needed a MK 440 PCL or the 460 PCL, but to have Ampere Time review the spec's and see if they are compatable, as all lithium batteries are slightly different

I haven’t ever heard anyone say the digital series is compatible with lithium’s, chalk that up to a Chinese company that is clueless. Even them saying that they must be disconnected before charging is stupid.

You need MKpc or MKpcl I think

Correct. The pc chargers will work (at least on Ionics) when set for AGM. The new pcl chargers have a lithium specific charge profile. I'd double check with your battery manufacturer on the use of a pc (precision) charger or go with the new pcl. The new chargers are now readily available.

I use the 440 pc on 4 ionics and it works great. I did put it on a timer for 3 hrs. a night, over 3-4 days it keeps them at 100% without the trickle maintenance charge.
they are bluetoothed and I don't trust the boat storage power to not surge at times.