Different output from essentially Identical IDML for different output types

I am testing a website enhancement locally that uses ID CS6, which i have running via the command prompt. The page first displays a .jpg preview of the file you are designing which is working correctly. When the user is finished editing the document they save it to a PDF but that PDF never matches the jpg in that a group of fields are always missing.
I extracted all the contents of the IDML files being used to generate the two files and combed through them and they are essentially identical. The only difference between them is any reference to the file path of IDML file and the file type I am passing to ID to generate.
Here is the JPG
And the PDF
I can provide exerpts from any file found within the IDML if it will help.
Any and all help is appreciated!

So I found the solution to this myself.
When I was comparing the XML files found within the IDML I wasn't concerned with XML syntax as all the files were valid XML. Whatever InDesign Server uses to parse XML apparently does not conform to XML standards because it does not parse this correctly:
<TagName Attribute="Value"/>
It requires the following syntax instead or it doesn't seem to parse correctly causing botched content generation like that seen in my OP.
<TagName Attribute="Value" />
Hopefully this helps someone else down the line.

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