There is no background running for LISP. It's either the AutoCAD UI or LISP, not both. This might be some of the fall-out of moving towards the "core console" concept where they further divorce the program contents from a specific UI like Win7. It allows them to better migrate program features to Mac but in theory it could also greatly simplify migrating to newer versions of Windows as well. Regardless, if there wasn't some wait-cursor-symbol, the user would still be unable to do anything but think the program had locked up.
If you want a status update for extremely long loops, have you tried the (acet-progress-ui...) functions? It might also be time to review and refactor the loop with an eye towards better optimization.