Same problem here, I have try on fresh install and upgrade from 5.2.8, same issue...
ePO 4.6, EEPC 6.1
I was helped partially with the following KB.
I am able to loggin in by using the user name shown in EPo> Encryption User>Name instead of the windows ID that I registered in Active Directory.
But, I still have problem that only users that I made in the preious day is working. User that I made an hour ago is not working.
I am curious about the mechanism of updating user in EE, after we update user EE User in EPo. I wonder whether a simple agent wake up call is enough to synchronize EPo and EE client, or maybe a client task need to be running. It look like I cannot found a detailed documentation on this.
Anyway, hope the KB may help you a little bit.