Hi dbjung,
I had the same problem.
The datasheet of Max10 ADC ("MAX 10 Analog to Digital Converter User Guide" pag.4) asserts that if you have a DUAL SUPPLY MAX10 FPGA you have to connect the banks where the analog inputs are placed to 2.5V power supply and you can supply an analog signal between 0V to 2.5V; instead on BeMicro Max10 all the banks are supply with VCC3P3, that is 3.3V (see the schematic of BeMicro pag. 5). This is wrong!
Remember that on the BeMicro MAX 10 the voltage reference is correct at 2.5V;only the power supply of the banks where the analog inputs (1A and 1B ) is not correct!
To resolve this problem I've changed the VCC3P3 supply in to 2.5V (I've changed the resistor RP4 connected to the power converter EN5319QI at pag 8 of the schematic) in such a way that the banks 1A and 1B have the correct power supply (obviously even all other banks now have 2.5V power supply).
With this trick, you have no longer offset of 350 when the analog input is 0V and you have 4095 when the analog input signal is 2.5V.
I've found that BeMicro has another error in timing of power sequence (it is different from that one recommended by Altera) but this doesn't matter with ADC results.
Bye.