Such a shame you had to resort to factory resetting your device because of a bloody android app.
I found the easy fix as I was faced with the same problem out of the blue, no contacts seen by whatsapp which I have to point out happens also quite often on android devices, the problem was with dalvik as a whole since even Facebook lite had no access to my contacts.
As I said, I found the ridiculously simple fix.
1. Go to android support in Settings
2. Un-tick "allow android apps to access my contacts"
3. Restart android support
4. Tick "allow android apps to access my contacts"
5. Voila!
Launch Whatsapp and refresh your contact list... But you have to be patient as it will take a bit of time to get contact list ready. Worked perfectly well for me, and I hope it saves factory reset for a lot of folks, as I hate the idea o resetting my device, to much stuffs involved