If you are seeing the correct voltage when using Test Panels and not when using the actual C++ code, then the problem is not with the DAQ card itself, but rather with the code that you are using. The problem could be related to using an incorrect input mode. If you look into the AI_Configure function you will notice the parameter inputMode which can be set to Differential, Reference Single-Ended, and Nonreferenced Single-Ended. Depending on how you are trying to transmit the signal will determine which of the input modes you should be using.
You may also consider performing a self-calibration on the device to make sure for optimal settings in the current environment your application is running.
The final think you should check is whether you get the bad readings when measuring a single channel in your code. You mentioned that you are trying to read from AI 0 and 1. The offset that you are seeing could be caused by some residual voltage that is left because you are trying to read the channels at too fast of a rate.
Good luck.
Jared A