Im also having this issue and Ive been searching for a solution for the last few days but I couldnt find one.

Basically once you set ignore:(+ new Date()), the uploader uploads to the old non-ignore collection. You can verify this by manually setting ignore:null after an upload and seeing that the upload appears again. The downside to this is that it loads an old cached collection so you lose the refresh functionality.

I did manage to figure out a workaround using collection.reset() but its not perfect as it clears the gallery during upload. But once the upload completes everything renders correctly again.

// this runs once upload starts
wp.media.frame.on('library:selection:add', function() {
    if (wp.media.frame.content.get() !== null) {          
         wp.media.frame.content.get().collection.props.set({ignore: null});
        wp.media.frame.content.get().collection.reset(); // this is the missing link
    } else {
        wp.media.frame.library.props.set({ignore: null});
    }
}, this);

wp.media.frame.on('open', function() {
    if (wp.media.frame.content.get() !== null) {          
        wp.media.frame.content.get().collection.props.set({ignore: (+ new Date())});
        wp.media.frame.content.get().options.selection.reset();
    } else {
        wp.media.frame.library.props.set({ignore: (+ new Date())});
    }
}, this);

edit: ok after working on this for the last hour ive finally found a solution that works without affecting uploading and without messing with ignore or reset

wp.media.frame.on('open', function() {
    if (wp.media.frame.content.get() !== null) {          
        // this forces a refresh of the content
        wp.media.frame.content.get().collection._requery(true);

        // optional: reset selection
        wp.media.frame.content.get().options.selection.reset();
    }
}, this);