Hello lethuer,
We have modified your example and we were able to successfully read some ADCB converted values with Freemaster, so I attached the modified example. If you will run it, please be aware that in order to read data using Freemaster we had to change your fault PTE1 pin with PTE2 (PTE1 is the TxD pin on UART1 used by Freemaster).
To answer your question, the Index from the ADCB must start from the value 8. So all ADCA channels must be consecutively indexed between 0 to 7, while the ADCB channels must have an index between 8 and 15. In your case the indexes should look like this:
(0, 8) - ANA0,ANB0
(1, 9) - ANA1,ANB1
(2,10) - ANA6,ANB6
(3,11) - ANA2,ANB2
(4,12) - ANA3,ANB3
Now, after we changed your indexing we found the following issues:
Simulink generates the code by ordering the blocks after some priorities that can be edited by right clicking the block and adding a number like in the figure 1.

Fig. 1. Changing the Block priority
In your model, the conversions were scheduled like in the figure 2. The program was waiting to get the value from the channel ADCA_CH6B(priority 16) but the ADC_Start2 block was never called (priority 55) so no conversion was started. This was happening because some blocks had some priorities, others none.

Fig. 2. Bad block priorities
The ADC should work like this: the ADC_Start0 must tigger a conversion and after it is done, the blocks under the ADC_Start0 must put the values in V_in and U_dcb/2 values. Next the ADC_Start1 triggers another conversion and so on. We reordered the blocks like in the figure 3.

Fig. 3. Reordered blocks priorities
Now, we found another problem caused by the IAR compiler, which reordered some program lines while otimizing the code. We fixed this by changing the optimization -Oh flag with -Ol or completely removing it. To test this you can change it on the Target Compiler Opts as in figure 4.

Fig. 4 Changing the optimization flag
Finally, we were able to read some converted values using Freemaster.

Fig 5. Freemaster reading ADCB values.
Hope that helps!
Marius