Could you please clarify if you mean the Agent module? If this is the case, could you please double check if you have the Run after reboot checkbox in the Agent window selected before a machine is rebooted?
Could you please clarify if you use the RDP-over-ID mode? If this is the case, the issue might be caused by a firewall. If your Windows Firewall is enabled on the remote PC, please make sure that the public checkbox is selected for "Remote Desktop" in the exclusion list: In addition, please check the RDP settings on the remote side, namely the security settings. They might be too restrictive to allow the client to connect.
In order to save bandwidth/traffic, the session may pause automatically, especially if you minimize the Full Control window. However, it should unpause and get back to normal when you return. Could you please verify that Pause/Unpause manually is working in your case? Here is a corresponding toolbar menu item: