We just upgraded one of our two 3600 appliances to R3 and when we launch the Backup Exec Administration Console from the Web GUI we get "Access Denied" the same as if we tried to RDP directly to the appliance.
Using powershell to enable remote desktop for troubleshooting no longer works either.
We have a case open but have not had a call back yet and we are unable to run backups so this is kind of critical.
Did the upgrade complete successfully? If not can you please check this : Remote powershell error when attempting to upgrade Backup Exec appliance 3600.2/R2
If not, it is better to wait for a Support Engineer to get back to you on your open case, as a debug might show some additional errors which may help in resolving the issue.
As an alternative way of connecting you can you use Backup Exec remote admin console (which you can install on a workstations etc) to get in control of your backups again. You can also setup the RMM3 interface for this. How to is detailed in the admin guide. As Ananya indicates, please get in touch with support on this.