You may not connect an ac voltage directly to the unit as the input range is 0 to 2.5v dc. You may however, connect a dc voltage that represents an ac voltage.
With respect to your second question, what type of signal are you monitoring and how is it connected to the ADC-11?
If you send a copy of the .plw file for the recording session in question for my attention to firstname.lastname@example.org
, I will take a look to try and understand what you are seeing and why.