Didn't know which of the posts to reply to regarding this but just to confirm that this also happens for me with WordHighlighter enabled, and doesn't happen with it disabled.
For those wanting to reproduce it's quite simple. First off it appears that scroll_past_end needs to be false, and WordHighlighter need to be installed and not disabled. But the actual bug occurs when you have a file that goes over the height of the window (thus invoking scrolling), and if you are scrolled all the way to the bottom and then delete lines. (Actually you could also be not scrolled quite to the bottom, but delete a number of lines that is greater than the number of lines left off-page.) Then, until you next scroll, the bug happens. Upon scrolling, the layout appears to reset itself.
So this could be a bug not in WordHighlight specifically but it could be that the WH plugin is exposing an underlying bug in the view/scrolling code. (Or yeah it could just be WH.)
This definitely only started for me a couple of dev releases ago. I've been meaning to bring it up but keep forgetting to.
There's also a long standing bug of the minimap not being updated for code folding until there's some kind of repaint (scroll action, of focus goes out of Sublime window, for example). This is not a biggie as you can just scroll and it updates, but just worth mentioning.