I am getting the same problem with firmware 3.3.0 and openpgp applet ver 1.0.8.
I tried updating the openpgp applet but i don't know the card manager keys.
I am aware of the security advisory YSA-2015-1, but it's my understanding that it should not affect encryption/decryption.
Is there a way to update the applet or fix this issue?
[Fixed]
I finally resolved the problems by unblocking the pin and changing the pin to something else. (previously i was setting the same pin after unblocking but that did not work.)
I was also getting errors with CHV2 on 'verify' command. I wasn't able to generate new keys and also getting "Conditions of use not satisfied" on some commands and couldn't authenticate SSH sessions or sign other keys... Which lead me to this tutorial
http://25thandclement.com/~william/YubiKey_NEO.html that pointed out some similar issues fixed by unblocking the pin.