Case 1: Negative values are within the range of acceptable values.
e.g. If you set up Surface Profile as Min = -0.0025 and a Max = +0.0025, you will get some negative readings and some positive readings from your CMM. In this case, 1factory will compare the actual value against the spec without converting to absolute.
Case 2: Negative values are NOT within the range of acceptable values.
e.g. Linear Dimension set up as 1.500 +/-0.005. While the expected values are all positive, your CMM may still output negative values depending on the location of the origin/datum of measurement. In this case 1factory will compare the absolute value of the measurement against the spec.