Battery imbalance - two 12v lead-acid 100ah in series
Yes, you do have a problem.
Series-connected batteries should be balanced, otherwise you always overcharge one of them and over-discharge the other. Neither is good for the battery life and you also get less cycle capacity.
Ways to solve it:

A balancing device. A search for &quot;24v battery equalizer&quot; will get you some ideas.
Charge the batteries in parallel (once, before connecting them in series). The batteries may gradually disbalance over time, but the process is slow and generally negligible for sane batteries.
Use &quot;Balancing charge&quot;. In essence, it is a mild overcharge that gets every cell charged to the max while overcharging the already charged ones. Rather harsh and makes batteries to lose some water, but does the job. It also equalizes the cells within the battery. Some controllers do this once in a while, some batteries don't like it very much.

The normal imbalance for a 12v lead batteries is less than 0.5v when charged and way less (less than 0.1v) in intermediate state of charge
p.s. I expect brand-new lead batteries to be of equal (near-100%) state of charge.
Getting two unbalanced batteries means something is not absolutely OK. Either one of the batteries has higher self-discharge, or the batteries are from different batches and were stored for different amount of time.