Having transparency and spot colors in PDF files can cause issues when rendering the output with various RIPs and applications. If you are trying to use a master PDF with both transparencies and spot colors for your eDocBuilder Interactive Designer templates, you might be seeing issues with how the previews and production files are rendering the output.
The recommendation is to include transparencies in the master PDF used on the template, but not to include the spot colors in the PDF. For the spot color elements that are in the PDF, you can try to convert those to CMYK. If converting them to CMYK is not an option then you could create fields for those elements and then assign the spot color label to those elements in the Format tab of the field on the Field Setup window.