Hi Matt, I can help you out with this. When it comes to exporting to .pdf, it could several different things. First thing to check is to make sure you are using the Mapinfo PDF driver. You can find the window in the Pro menu, then options, then Printer.
See Attachment
In terms of the layers displayed, you should be seeing anything "check" on in layer control. Hopefully you are creating a layout first before exporting. Is this so? Or are you maybe exporting from the Map window?