However I was saving the files as "Save as" and then choosing to save them as pdf.
Oh, well that at least explains part of the problem. I don't know why the cairo png was creating that fadeout effect, but it must have started there. Maybe it didn't know what to do with the masking? I'm not sure.
You would never use Save As cairo png. It will be removed soon (already has been removed in the development version). (Removed because too many people were using it without really understanding what it's for - just like you. You were definitely not alone!)
The preferred option for sending something to a printer is to ask the printer what format they require or prefer. Printers often have their own preference for which format they use, based on their own experience, and often based on their hardware. If they want an SVG file, you can email an SVG file.
All the different file formats have their own pros and cons. PDF is usually used for creating professional documents, and for professional printing. In fact, Inkscape's native printing capability is so basic, that we often suggest users save as PDF and print from their PDF viewer (if they need anything more than a very basic print).
Also, different formats support vector contents differently. PNG is strictly a raster format, and you would never use it if your project requires vector graphics. Some formats are strictly vector, some strictly raster, and there are a few (such as PDF and SVG) which can contain both raster and vector contents.
Wikipedia probably has some basic info about comparing the graphic file formats. Let's see.... Maybe you want to bookmark this:
https://en.wikipedia.org/wiki/Graphic_formats
