I just tested my branch in Unity desktop environment of clean installed ubuntu 16.04.
but, I cannot reproduce problem...
For your reference, I uploaded video clip.
Some visual glitch is same(around ellipse tool)
but mouse input correctly processed...
My main PC is DIY one, and this test is done in VAIO T laptop.
Mypaint branch is downloaded from github as zip file, and extract it in VAIO.
I use wacom intuos CTH-680 and logitech mouse m100r and m325.
Have you installed any additional desktop programs?
Both of my tested environment are almost vanilla one.
Or, possibly, something changed(enhanced) in GTK3, and it might affected to my codes...
Actually My experimental tools (exinktool and beziertool and polyfilltool) are largely changed from vanilla mypaint, that changed parts by me might not follow gtk3 enhancement and things going wrong.
I'll continue researching around such thing.
Anyway, thanks for your reporting