I patched in the Kemper as an outboard effect in Cubase, and Cubase measured the latency and compensated (as it does).
Which I do exactly the same way, see my post above. Nevertheless I do not have the phenomenon you describe. If I record DI/Stack on two tracks and then reamp the DI track with the exact profile I get exactly the same "wet" track. And if the latency compensation did the job well they are so well aligned that they eliminate each other if I flip the phase of one "wet" track. Silence then. Perfect for me.
So what goes wrong where?