I can confirm that this is a very annoying issue that needs to be fixed as soon as possible. When you write words, and use "i", "l", "t" and other letters, eventually it's inevitable you will make a perfectly horizontal or vertical line, triggering this annoying issue.
I have some information that should help to solve this issue:
1. If you look at the merged PDF file on a computer, you will see that perfectly horizontal lines ARE there.
2. However, if you zoom in these horizontal lines on a computer, you'll notice that they are infinitely thin.
3. Thus, horizontal lines seem to be merged on in a way that does not account for the thickness of the line (similar to vector graphics
4. The problem isn't that the line isn't there. It's that it's infinitely thin. If you then convert this PDF (which does have horizontal lines) file into an image file, you'll notice that the horizontal line are now gone at normal zoom.
5. If you zoom into the image file, you'll see that the horizontal line is there but very thin and very faint.
So the problem seems to be that the PDF created by merging treats perfectly horizontal lines as an infinitely thin line. Thus, this is partly a display issue. Since the horizontal lines are in fact on the PDF file, a possible temporary workaround would be to make the M92 display these lines properly at normal zoom, like how a computer is able to.
Here's an alternative temporary fix that can be implemented: merging the scribble should create an image PDF, basically taking a screenshot, even if that causes, say, text to be no longer highlightable due to it being an image. E.g. the Scribble application exports to PNG, so it doesn't have any problems with horizontal lines. So merge PDF annotations by creating a PNG like the Scribble application, then convert the PNG to a PDF.
The permanent fix would be to give the horizontal lines thickness like all other lines and make the thin lines display properly like on a computer.
Let me know if you need some samples or screenshots.