I have a single (no satellite or additional primary) Windows 2008 R2 server running ZCM 11.2 and I upgraded it to 11.3a. The upgrade process went smoothly with no errors and a required reboot after. After the reboot I logged back in to ZCC web and it gives me the following dialog.

Your zone is being upgraded to ZENworks 11 SP3. However, the following Primary Servers in this zone have not yet been upgraded to ZENworks 11 SP3. You need to take these servers offline, and manually upgrade them at the earliest.
Note: If any of these servers are in the process of being upgraded, you can ignore this warning. They will be removed from this list once the Agent refresh is completed.

zen01 is my one and only server. The Adaptive Agent (v running on the server is the only portion that appears to have been upgraded.
ZENworks Configuration Management Version:
ZENworks Asset Management Version:
ZENworks Patch Management Version:
ZENworks EndPoint Security Management Version:
ZENworks Full Disk Encryption Version:
ZENworks Agent Version:

The server in ZCC indicates it is awaiting a reboot
zen01 Now Prompt User Awaiting Reboot Server /devices/servers/zen01

Everywhere I look it indicates it is waiting for or requires a reboot. Needless to say I have done this several times. I have also ran the upgrade again and it indicated that it was already installed but allowed me to continue anyway. I have also tried the upgrade with all Novell services stopped with no luck.