Comment 3 for bug 1331549

Yes, maybe a delay. Or Onboard auto-hides when typing with physical keyboards. Or both. Total coincidence, but that hiding is what I'm currently working on. There's a possibility that your mouse Shift press would cause it to hide too (if it doesn't go through the XTest device) so you won't see the shift keys, but you would be able to turn hiding off in preferences.

One more thing, no matter if Shift_L or Shift_R was pressed, you'd always get all shift keys highlighted in Onboard. The X modifier state we get has only this one Shift bit, unfortunately.