You will likely need to reskin the layout and use one of the themes in order to correct the rendering issues. WebDirect works much better using the CSS-based layout system than the old object-based one.
I've been reading through the FileMaker WebDirect guide, https://fmhelp.filemaker.com/docs/14/en/fm14_webdirect_guide.pdf. There's a lot to do on a layout to make sure it is WebDirect compatible.
The biggest question is: Are all your objects on your layout set to a style within a theme? Web Direct, I gather, really prefers saved styles over local styles.
That might be a place to start.
look up the richard carlton consulting video on optimizing for web dirct