Comment 6 for bug 1374301

I see this too on a HiDPI display. I was able to workaround it by using Steffen's suggestion:
$ sudo cp /usr/lib/x86_64-linux-gnu/notify-osd /usr/lib/x86_64-linux-gnu/notify-osd.real

Then creating /usr/lib/x86_64-linux-gnu/notify-osd with:
#!/bin/sh
set -e
export GDK_SCALE=1.0
exec /usr/lib/x86_64-linux-gnu/notify-osd.real

Then:
sudo chmod 755 /usr/lib/x86_64-linux-gnu/notify-osd

Test with:
$ sudo killall notify-osd
$ notify-send test

Note: once you are using the above wrapper you will use 'sudo killall notify-osd.real' instead.