After working on this problem for some time I have found out what was causing the errors. It seems that Visual Editor was a bit more forgiving when parsing the code to display the preview.
My issues with Window Builder generally stemmed from the following things:
- lack of paramterless contructors in both the panel/dialog to be displayed and components within. WB relies on these constructors to parse the code
- trouble getting dynamically generated resources which led to throwing null pointer exceptions. Visual Editor seemed to ignore these and display what it could. Window Builder would not display any part of the offending component. Adding null checks in certain places remedied this.
After fixing these problems, I did not have to recreate any of my GUI screens in Window Builder