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Scenario:  

Client machine is joined to Azure AD, and logged in Azue AD user account used to deploy SES 9.0 SR2 with MagicEndpoint Enterprise enabled. 
MagicEndpoint Enterprise client is installed and linked to SecureDoc successfully. 

Steps to reproduce this issue:
On SES server, upgraded SecureDoc Enterprise Server to V9.0 SR3 and the MagicEndpoint IDP was upgraded to V9.0 SR3.
2. On SES, create a new profile 
3. On client, the client was upgraded to V9.0 SR3 and upgraded ME build to 1.3.1.
→ MagicEndpoint is set to automatically login, and the MagicEndpoint IDP status is “Online“
4. Launch the IDP page
5. Login to the IDP page
6. The expected results should be:
User should be able to login to IDP after upgrading MagicEndpoint

Actual result:
Failed to login IDP page at first time after upgraded ME with error message:
"Unable to authenticate using MagicEndpoint client. Either MagicEndpoint authentication failed or it is not installed on this device.
If MagicEndpoint is installed but failed, re-try authentication manually. If not, authenticate using the WinMagic Authenticator phone app."

Low-effort work-around:
Try to reboot/shutdown the IDP web server's Login page.  Using this, users were eventually able to login to the MagicEndpoint IDP web page, though several retries may be necessary.

NOTE:  This bug does NOT occur on a fresh SecureDoc 9.0 SR3 installation.

Better work around:
The following is a more certain way to correct this issue: 
After MagicEndpoint has been upgraded to 1.3.1.
1 - Open the Windows Control Panel app.  
2 - Click on Internet Options, then select the General tab.  
3 - In the General tab's section entitled "Browsing History", click on the “Delete“ button. 
The "Delete browsing history" panel will appear.  
4 - Check all the checkbox options, Click the Delete button at the bottom of the "Delete browsing history" panel, then close the Internet Properties panel. 
5 - Open your Chrome/Edge browser application → Go to Setting → Select “History“.
6 - At the History tab → Select the “more options“ icon → Select “Clear Browsing data“
The Clear browsing data menu is shown
7 -  At Time range, select “All time“, then check all options
8 - Click on “Clear now“ button
9. Un-install MagicEndpoint 1.3.1
10 - Re-install MagicEndpoint 1.3.1
11. Launch the MagicEndpoint IDP webpage,  then login to the MagicEndpoint IDP
→ At this point you should be able to login to the IDP page
12. Reboot/Shutdown the endpoint device, then restart it
→ Again you should be able to login to the IDP page