I've read your past posts.
With regard to the size of the batteries, the only think that could keep them from coming up to voltage would if you had a bad battery.
I have a 48Vdc system setup using solar panels and once the sun comes up, the meter show the voltage rising until my GHurd controllers kicks in.
My 48V system which is for an e-scooter uses free to-me 6V 7Ah batteries setup in 48Vdc fashion, so even though your system Ah is small you should still see voltages up above the dying levels.
When you get a calm wind moment, short the mills legs, pull the batteries off each other and see if you have a bad battery.
Let them sit for a good hour 2 or more would be better, then test each one separately, making sure they are at the same voltage.
Then if they are not at the same voltage take your best 4 set them up as 48V and reconnect the the controller and un-brake the mill to see how well everything works together.
Let the other batteries sit overnight if you can, and check to see if you have one that has gone bad on you.
Better to have 7Ah of 48Vdc than 0Ah of 48Vdc.
IF ALL batteries are okay, can still try letting the system charge this smaller setup.
Hope this helps