I'm a bit skeptical that it has to do with anything but the registry. Have you only tried this on the one system? The user has to register with the server, but in the logs, you are seeing things like:
[01/28/15 11:30:15][ERROR][1356][0x578][EAFRCliADSIComm][SYSTEM][ADSICommunicationThreadProc - LoadCommunicationData failed.][EADLL.cpp:262]
The failure to load communication data would definitely prevent a user from registering, which would prevent the drive from adding a registered user, which would prevent the Bootguard from displaying. I don't know that it bears any further troubleshooting other than trying to figure out what is wrong with the registry.
What security software or antivirus is in use? Security software can prevent registry entries from populating during installation. I will also continue to research in my lab and see if I can replicate what you are seeing.
One additional thing you may try is to manually add the user through the Command Prompt. Run cmd as an administrator and do the following command:
eedAdminCli --register-user --disk <number> -u <username> -p <phrase> [--sso] [--domain <domain>] [--admin] --au <AdminUserName> --ap <AdminPassword>
An example might look like this:
eedAdminCli --register-user --disk 0 -u "Bob Jones" -p Bobsp@55w0rd --sso --domain Ankeny.local --au ClientAdmin --ap CAdminp@55
I have found that this works fairly well for cases where there is something off about the hardware (i.e. some hybrid drives), and if it does work, it should allow the drive to encrypt. While I doubt this will fix the issue in its entirety, it should allow us to see if the issue might be hardware related.