In certain updates of Millau, the buttons and search bar are connected in headers. If there is custom CSS prior, it will override the declarative choice made in Skuid. Is this the problem you're facing? If you're able to post a picture, that would be helpful
My suspicion is that this changes depending on your theme. This also is largely impacted by the amount of space allowed. The fact the Search is underneath makes me think that the space is considered small and so it is automatically stacking. We highly recommend using the filter set and the search component inside of a responsive grid to give you the most granularity and ability to customize without CSS
I just updated a sandbox to the latest version of skuid, and was having this same issue. No custom CSS present. I then remembered the old "update out of date themes" button, and that got it sorted out for me.