I tested this before my post on my Glo HD with firmware 3.19.5761. Did you make sure the spaces were between the sentences?
The code the extended driver generates looks like:
Code:
<span class="koboSpan" id="kobo.3.1">Sentence one.</span> <span class="koboSpan" id="kobo.3.2">Sentence two.</span> <span class="koboSpan" id="kobo.3.3">Sentence three.</span>
The kepub bookmarking uses those spans and the ids. If the start or end of a selection is outside the spans, then the highlight cannot be save. Selecting the space between the spans as the start of the highlight will trigger this. A side effect of this is that when you select across the space, say from the word "one" to the word "two", when the highlight is drawn after it has been save, the space between the sentences is not highlighted.
To see this, put the attached kepub your device. This has been converted from an epub. Then I edited the "Forward" to move the spaces between the spans into the spans. If you select a sentence and make sure you include the space before it, the highlight will be saved.
If you go to the chapter "Font Display" and do the same thing, the highlight won't be saved. And if you do a highlight that goes from the middle of one sentence to the middle of the next, the highlight will be saved, but the space in between the sentences won't be marked.
To make this easier to do and see, I also edited the first paragraph in the chapter "Special Characters". In this case, I removed the span wrapping the second sentence. If you try to make a highlight from somewhere in the first sentence, to somewhere in the second, it won't save. Or from somewhere in the second sentence to anywhere else in the chapter, it won't save. And if you select from somewhere in the first sentence to somewhere in the third sentence, the highlight will save. But, when it is redrawn, the second sentence will not be highlighted.
From what you are describing, there might be something else going on. But, it is a problem and eliminating it might expose the real problem. And it is possible that these errors are causing other problems in the highlighting engine (memory leaks etc) and eliminating these errors will mean the other problems don't occur.