I've tested a FlashScan here with the same firmware and the A/D inputs work correctly. If the raw A/D counts are not getting up to around 700-800 at 5V then it is likely something has failed in the A/D hardware.
It probably needs to be returned to EFILive or SoCal Diesel (EFILive's US based repair facility) for repair:
https://www.efilive.com/distributors
The fact that all 4 A/D inputs have failed in the same way at the same time does make it appear like it is a firmware problem. However it may just be a configuration problem. Try clearing FlashScan's configuration using this technique: While FlashScan is powering up, hold down the F1 button. That will revert all the configuration data to factory defaults (excluding the A/D calibration values). When you do that the blue LED should flash to indicate that the settings are being erased and reset.
The unit I tested with here had the factory default settings. The settings that I am referring to are the ones you can edit/modify in the V8 [F6: Devices] window.
Regards
Paul