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It wouldn't work anyway since you're applying a filter to nothing, and the filter would be cleared when the new folder loads. You need to wait until the folder has loaded before you filter it.
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The two sides are largely independent, but can't be entirely as they do share the same window, status bar, toolbars, etc. It's also possible that shell extensions are causing problems, e.g. if they are not designed to be used in parallel by multiple windows and make each one wait in a queue if another makes a request that is slow.
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Turn on Preferences / File Operations / Progress Indicators / Minimize progress indicators and the option above it to display the jobs bar.
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The Customize dialog is on top of all Opus windows by default, not just the one that opened it. You can change that via the Keep On Top menu. Button Editors will remain on top of everything regardless, because they have to be able to edit things on menus and on-top windows and would sometimes end up lost behind the thing they are editing otherwise.