You cant control the names of the form elements that CSS Form builder will create, so it will not create the forms using the correct names.
After the form is created you can rename the elements to work with your pearl script.
as for the validation, did you uninstall validation toolkit before installing css form builder?
are you using client or server side validation?
can you send a sample of one of the pages you cannot apply validation to?
A screen shot demonstrating the problem would be helpful as well.