We’ve seen this in our version (10.1.600.20) . It seems job entry is opened in a modal type of mode (how dya like that description?!) when done via planning workbench. We greatly hate this new feature.
No, there’s no way to shut if off that I know. I think a customization of the planning workbench to perhaps hide original button and make own button to open job entry could work. The parameters would need to be passed to get on the right job. We live with the bug and have not dealt with it.