Call Stack and Watches panes keep reappearing

[kinook]

It should use the layout you exited with the next time you start. Normally, there is a separate layout for design and build mode, and each needs to be configured separately (so you would need to close the panes in both design and build mode [press F10 to begin a build and pause at the first step] to never see them), or you can uncheck Tools | User Options | Use custom pane layout when building to always use the design layout.