It's been a while since I have tried making a lot of annotations in a sideloaded kepub. I don't think I have anything suitable on the device at the moment, so I'll add one tonight and test.
But, just in case it is something about the annotations you are making:
What are your annotations like? Single words, sentences or across sentence boundaries. Long ones that go across paragraph boundaries or other tags.
Are the all in one chapter or spread over the book?
Does it matter if they have annotations or are just highlights? Are you annotations long?
What if you just bookmark 20-odd pages? By that I mean tap the top-right corner for a dog-ear bookmark. (Which makes me think of
https://www.mobileread.com/forums/sho...postcount=7087).
Are the books likely to have complex markup? Novels are usually simple, though some book creators seem to go out of their way to make their life hard. Text books are more likely to have complex markup. They will probably have more tags and are likely to have nested tags.
Have you checked the annotations list? There is one circumstance for epubs where the highlight for the annotation isn't displayed after making it, but the annotation is in the list. Because of why the problem happens, changing the reading settings will usually cause it them to be drawn properly.