Having trouble rendering the exact dimensions in web printed PDF

[ghxstweb]

So I have made a fork of this repo and have been working on augmenting it significantly, giving it a ton of new features, etc. However, when I try to print to PDF, the actual document does not render 100% correctly and the final PDF copy that I download has some rendering artifacts. Here is an example of what it is supposed to look like:

Notice the space between my page indicator and the boxes?

Here is what the PDF looks like, it's a bit messed up (notice the artifacts, circled in orange, and the reduced distance between the page indicator and the boxes):

Can you help me fix this issue @ocram ? I would really appreciate it!