Small square boxes appearing on blank lines (UPDATED) - The question is, how to get rid of them?

Question

*******  As to my display name "All I tried were in use" - when I registered at the Adobe site to use the Browser Lab, I tried something like 10 or 12 user names and finally gave up and went with "All I tried were in use" - my name is Bob
------------------------------- UPDATE --------------------
The problem, small square boxes showing on lines in Freetext Tool comments, is not limited to blank lines, as I originally reported here. These boxes are showing up at the end of every line. It does not matter if the line break is hard or soft, whether the line is empty or not.
Please read the original post bearing mind that the  problem is occurring at the end of all lines.
Also - here is a screen capture of a part of one comment box, showing the square lines. I didn't show the entire box because the material above the area I'm showing is a tad private or confidential. Here is the image showing the boxes - note that there is no box at the end of the last line in the comment.
-------- Original Post ------------
We have a copy of Acrobat 5.0. and up until now it has done what we need, which is not much more than adding bookmarks, links, and some touch up. I know it is very old and I know things change. I'm hoping this has nothing to do with the release we are using. I would think this would be a backward compatibility issue if it is a problem with newer Reader versions dealing with PDFs "edited" with 5.0.
I am having small square boxes showing up on blank lines. (read my update above  - the boxes are at the end of all lines, soft break or hard break))
I'm a programmer (37+ years in most all aspects of Data Processing) and I decided to learn the PHP programming "language" to add some server side processing to some of my web sites. So, I found a fairly good manual on PHP in PDF form and have been using it.
I quickly found that the PDF didn't have a single link in it and no bookmarks, so I've been adding them as I look up a particular subject. I'm also adding comments and notes to document things not in the original manual or to add comments that would help other programmers` (who know  other languages) to adjust to PHPs' way of thinking - for example: in all the other languages I know (perhaps two dozen) to get rid of a file, you "delete" it. In PHP you "unlink" it.
I've added a lot of comments and notes like that and when I view the PDF in Reader (on this computer I have 9.4.2) I'm seeing small square boxes on empty lines. The lines were created when I pressed Enter twice to insert a blank line between paragraphs. (again, read the update at the top of this message - the boxes are at the end of all lines, soft break or hard break)
How can I get rid of them?
They are not present when I've got the PDF open with Acrobat, only when I'm using an Acrobat Reader.
They are also not present if I look at the comments using the Comments navigation panel - that is, they still show on the page, but they don't show in the copy of the comment displayed in the navigation panel.
They are not present in Notes or when I use one of the shape tools (Square Tool, Circle Tool, or Line Tool) to create notes. They are only present in Freetext Tool comments
They are clearly being show where there are successive line feed/carriage return characters - but how do I get rid of them?
I JUST THOUGHT OF SOMETHING - I realized that I'd not printed any of the pages on which I have placed comments and wondered if the boxes show when printing the PDF with Reader -- they do. They are not present if I use Acrobat, not a Reader, to print the same page.
Any assistance you can provide will be greatly appreciated.
Please don't tell me to get a newer version - an expenditure like that is simply and totally out of the picture. For us, this is a Depression, not a Recession - we are self-employed and our businesses have been severely hammered since 2006 - we are down to about 1/4 of our income before the big guys trashed the economy.
Bob
P.S. Do you know that you can have a heart attack without chest pain, shortness of breath, or left arm  pain? Well, you can! I've had two and the first one nearly killed me because I had no clue it was a heart attack. You can read about it first one here.  Pass this on, it could save a life.
My second heart attack occurred on October 4, 20112 - it began, around 3:15 AM, as the first one did, with a headache. It turned out the stent implanted in 2002 had been completely clogged by too much tissue grown. The doctor put another stent inside the first one.

Answer 1

Problem Resolved - it is a font issue. Apparently Acrobat can't handle particular fonts and it is best to stick with a very small slection of fonts - Arial, Helvetica, Times Roman.
I haven't test a lot of fonts. If I do, I'll post there results here.
Bob