after weeks of suffering with this, I may have found the issue.
I found another thread mentioning this issue occurs when Cursor is not the selected window when the agent finishes. Running an agent and ensuring Cursor is the selected window seems alot better.
I think the issue is windows notification, which is triggered when cursor is not the selected window. Since turning the notifications off, I’ve not been getting any freezing (for now).
Hope this helps, please try 