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When comparing results across two scenarios, the nodes change order depending on how you've sorted the columns in the first scenario so you're not looking at the same nodes and how their result has changed.
e.g. if looking at changes in velocities from the base run to the new scenario, arrange the base scenario link results by max velocity; then drag on the new scenario, but instead of the node ID staying in that order, the max velocity stays arranged by max velocity and the nodes have changed so it's not comparative.
Thanks for the input. As this gathers votes and consideration in our backlog, there are other approaches you can consider when comparing scenarios.
If you open one simulation, and open the other as alternate results for comparison, you can run SQL Queries or even custom themes on expressions like the following:
select oid, sim.vmax, sim2.vmax, sim.vmax-sim2.vmax AS [Difference]