Solution
The analog trigger circuitry on the S Series device is responsible for the offset. A given signal runs through the Analog Trigger Comparator (ATC) before running through the Analog to Digital Converter (ADC) as seen in figure below.
As you can see, a signal going through ATC, then through the ADC will actually be adjusted to a different value in order to account for gain error in the amplifier. There are also inherent gain and offset errors in the ATC circuitry which are not calibrated out. If you need accurate analog triggering with a S Series board, you can use analog events or conditional retrieval to accomplish it in software. Refer to the links below for more information on how to do this.