This problem is unique to Boxcryptor. In particular, it does not happen with Google, Dropbox, Dashlane, or Vanguard.
I'm having the same problem as derNeue, but with the Yubikey Security Key. (The key is blue.) I went to the link that Oliver listed above. It did not appear to have anything to do with Yubikeys, and it did not provide a solution. Interestingly, I have the older generation of the same Yubikey and Boxcryptor didn't require a PIN when I re-registered it. I have two of each type of key and they each do the same thing so this is not due to a defective key.
I would really appreciate it if support could provide some help. My wife is not very computer literate and this is creating confusion since it is only happening with half of our Yubikeys and only with Boxcryptor.