Pico Staff might have some comment on this, and knowing which scope you have would help I'm sure... but ...
I'd suggest you check the earth of channel A, if comparing with a volt meter (DMM) tap into the back of the stackable 4mm leads, then you know both scope and DMM are seeing the same data. Critical for any scope to have a good ground (battery terminal not the chassis etc - could be volt drop ie during cranking) but if you have the new floating earth scope, even more important.
Second, try restarting Pico software, while not loaded, unplug and replug USB, so software starts with Pico Scope already connected, maybe to a different USB port...
Third go back to a pre 6.11.xxx version, maybe even 6.9.xxx and try that? I've rolled back to 6.10 on one machine and will probably go back to 6.9.xxx as finding some massive issues with 6.11.xxx release ... not sure if it will help, but worth a try if all else fails.