Operating system: Kubuntu 18.10, 4.18.0-22-generic #23-Ubuntu SMP Tue Jun 4 20:22:46 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
Graphics card: NVIDIA Corporation GP106 [GeForce GTX 1060 6GB] (rev a1)
Broken: 2.80, 9c5d54bfaf48
If focus is in another application (e.g. a terminal window) Blender ignores any modifier keys that are depressed when mouse clicks and drags are executed on the Blender window.
E.g. If focus is in another application and shift-mmb drag is executed in the 3d viewport, it ignores the shift modifier and treats it as a mmb drag (i.e. it should pan, but it rotates the viewport instead.) Same thing with shift left click in the 3d viewport, shift left click in the outliner, alt+click drags, etc.
I don't think this is window manager related; it does not happen with other applications (e.g. with gimp it registers correctly).