By default the agent tray icon will not show if you are in a remote desktop scenario. You can see that in the agent logs - will not load it in remote session type message. The later 5.x extension for the agent adds a checkbox to allow the loading of the agent tray icon during a remote session. By default that is disabled. It can cause issues with citrix sessions where multiple mctray processes are running, which is one of the reasons for disabling that.
On a side note, from a defect opened on that, it appears to be resolved in the ma 5.5.1 agent.
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Have you been able to test the 5.5.1 agent that is supposed to resolve the errors you are seeing?
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