I have had a look at the code. There is no limit to the number of annotations it will retrieve. But, there is a problem if there is two copies of the book on the device. In this case, it takes the annotations from the first copy that is found. In the case I described, the kepub and the epub, this will generally mean the annotations will be taken from the kepub.
Is this the case for you? Do you have two copies of the book on the device? This will be shown in calibre in the "On Device" column. If there is only one copy, this column will show a tick and either "Main" or "Card A" (or something like that). If there are multiple copies, it will show "(2 books)" after the location. Is this the case for the book that is not getting annotations?