Code:
Are the 2 PDF's generated in 2 different ways?
Short version, Yes.
Long version ... J! is built around the MVC methodology - Model, View, Controller, where each page load runs a given view (like a Fabrik form view, or a J! article view, etc). So a component runs, loads a "view". This works great when all you need to do is render one view ... the CMS itself sets up everything for the "model" and the document, the view, etc and rendering is very straight forward ... but in the case of generating (say) a PDF view of a document, while you are already inside another "view" of the same form, is like trying to hammer a square peg into a round hole.
So we have to kind of emulate the entire process of what happens when you click that PDF button for a "normal" PDF view, within the code for the email generation.
That said, it's possible that your issue is not to do with the PDF generation, but something with the formatting of the data.
If you can tell me which form this is, I can take a look, although i can't promise anything. PDF document generation is a huge problem in J!, as Joomla itself doesn't provide it, and we rely on 3rd party libraries to do it.
-- hugh