Severe mouse slowdown/latency when transparent app is running

[emotion-engineer]

See these gifs. The first shows mouse movement when only the Unity editor is open, the second shows mouse movement when a transparent app running. There is an extreme slowdown in mouse movement, it is impossible to control accurately, and keeps moving for ~1 second after the input stops. When the mouse cursor is over the transparent app, mouse movement returns to normal. How can I address this?

Normal, no latency:

Transparent app, high latency: