I have two alignments that are identical with the exception that one of them has a station equation. After creating cross sections for the two alignments using the same surfaces, why do the end area volumes differ?
If the station lock is toggled on (Tools > Locks > Station), it is possible that the end area volume between the alignment with the station equation and without the station equation will be different. When this lock is turned on, the software creates the first cross section in the set at the first station and then forces all subsequent cross sections to even-numbered stations. When it encounters a station equation, a cross section is cut at the station equation and then all subsequent cross sections will be at even-numbered stations.
For this reason, the cross sections will be created at different locations along the two alignments. Since the surfaces are not extracted at the same location between the two cross section sets, the computed area and end area volume will differ as well.
If you wish for the two cross section sets to compute the exact same end area volume, you should turn off the station lock before creating the cross sections and take care to use the same cross section interval.