i will admit that as we not longer have a lorry with 24v i have not done this test, but the theory is...
i assume the batteries are wired in series right next to each other ? Therefore producing 24volts ...
Then the test should be using the 24v option not 12v, but testing both batteries together ie putting the probes across the terminals where the vehicles supply leads leave the battery area (one to chassis and one for positive to where ever it goes) ... did you look at the graph to see what you did capture? can you post you data file?
if you were to test each battery individually then use 12v and put the probes on to the terminals of only one battery at a time. however i am not sure this will give a true reading and have never tried it. you could not do the extended tests as volt drop calculations would be wrong.
if unsure, use a multimeter set to volts in the same position you plan to use the pico probes, the dmm will show how many volts you have at that point in the battery config. if you have your probes in the wrong places the program will not give useable results.
if you still struggle to get good results try a known good vehicle with similar battery setup, or try to just take a battery voltage vs amp clamp reading in picoscope over an 8second timeframe while cranking the engine to start ... you should see the volt dip as it cranks with amps peaking ... basically seeing the compression cycles of the engine.
hope you get to the bottom of it!