Editing Text

I am creating test medical records using pdf templates.  In these templates I have placed tokens that will be replaced with data.  For example {{patient_name}} might become "John Doe".  I will feed in a spreadsheet with a number of test patients and will generate documents. 

I am having a problem with how Acrobat is changing how I am organizing text.  Below is a sample of what I am talking about.

The bottom part was saved earlier.  I entered the text in a single text area.  It has split up into columns.  In this particular case it doesn't matter.  The "Vitals" section above it was added right before this screenshot was taken.  Below is what it looks like after saving and re-opening.

Here it has split up my token and I will have issues when I try to generate the final document.  Is there any way to make Acrobat stop messing up my organization? In many cases the token appears in a paragraph that must re-orient itself to handle the change is text length.  For the most part this works, but occasional I get results like the one above.  As a secondary question, what is the proper name for those little boxes.

Thanks,

Matthew