With JP25 [5-6] connected, BIAS_ELEC and REF_ELEC will be shorted together. Was this your intention?
Because JP6 = [1-2], the BIAS_ELEC signal is simply a mid-supply voltage buffered by U11. This would equal 0V because you are using dual-supplies (+/- 2.5V).
In contrast, the REF_ELEC will carry some DC bias and some local EEG AC signal (assuming you still drive the patient).
I'm not sure which option is best for your single-ended measurements: INxN = BIAS_ELEC (mid-supply), or INxN = REF_ELEC (DC+EEG). I would experiment with removing JP25[5-6] and use REF_ELEC as your SRB1 input. Connect the reference electrode to JP25[6] only. To buffer the REF_ELEC signal and give it better drive capability, use JP7[1-2] and JP8[2-3].
Lastly, you can always confirm your register settings using the ADC Register tab -> Register Map -> Refresh Registers.
Saludos!