I believe I have also seen this issue (or something very similar) on my Windows
7 64bit machine. I am running gpg 2.1.11. I hope this isn't redundant, but it
seems that I need to restart scdaemon anytime I unplug/replug my yubikey or
suspend/resume my computer.

Sometimes it doesn't recover even after restarting scdaemon. In those cases, I
am able to fix it by stopping scdaemon, removing the yubikey, starting scdaemon,
and finally reinserting the yubikey.