It sounds like you can adjust the search input width to fix this. The way you can set the layout for your site, the search and other widgets are not really able to simply adapt to their widths so using a narrower column and placing the widget for search it’s possible the styling is expecting a larger area.
You can add something like this to your Custom CSS area in the default design settings (Appearance > Design Settings)
#searchform input#s { width: 100px; }
Adjust the “100px” as needed to get the search to appear on a single line.