If your batteries are both connected to a rack busbar and then the busbar is connected to your inverter(s), then that sound's correct, and, baring a bad connection somewhere, there should be no difference between them. I think they are just at a different SOC, and, like I said, you need to get them both top balanced individually and then connect them together.
My test just ended with the inverter shutting off due to the low battery voltage setting, which I think I'm a bit conservative on. I'm sure the batteries still have a few kWh left in them, but they appear to be pretty close on SOC, and they maintained a pretty consistent current between them for almost 7 hours, so I'm happy.
