Hey again,
This is exactly what was happening to me and would also explain why I out of the blue had Synchronized Browsing enabled (Ctrl-W). I have changed my commands to Alt- and they now work fine. :-)
Ctrl-R with the queue window focused only works if a failed transfer is also selected. With nothing selected I'd expect the Raw Command to pop up instead. Though, I suppose this is an issue with any 'universal' command.
Maybe a future keyboard command UI where we could freely choose? Or a warning when we bind a command over a [universal] command already in use.
In the end, I'm glad this was 'solved' for me and I thank you deeply for your help.