I don’t have integrated graphics on the current PC, but I’ve tried with an old GeForce 740 and got the same results (stutterring when running with Visual Studio debugger).
Does your app have many models/shaders? Note that rdb said that a more GPU-heavy Panda3D app runs steadily for him. You can try running a more complex Panda3D program to test this. I would recommend this game A Door to the Mists--Demo released! by Thaumaturge.
Also, did you try disabling Nvidia overlay?