Before upgrading my Lumia 525 to Windows 8.1, WhatsApp worked very well, which means all the new notifications had received properly but after upgrading to 8.1 I’m not getting new WhatsApp notifications in the Tile or Notification section. I can get those messages after opening WhatsApp. I remembered one thing while upgrading 8.1 that Phone warned me that WhatsApp won’t work properly in this version. Is it possible to rectify this issue? Do anyone facing the same issue?
Try to re-install it.. It worked fine on mine... Delete -> Reboot -> Fresh Install .. Remeber its Windows ;)
EDIT (more details):
With a delete and a fresh re-install you also delete the settings and other artefacts/logs (stuff from previous versions) that are created other the time and gives you now these errors. with the reboot you make sure that these Data is removed and isn't used from the new fresh installed Whatsapp.