That's a known bug but you have the wrong cause. The correct chapter is being lost when you reopen the book.
The problem is that the annotations can be stored in two places. They are in the database on the device, and for epubs and PDFs on the main memory, they are also in a file. When an epub or PDF in the main memory is opened, any annotations in the file are merged with those in the database. Unfortunately, this is done in such a way that the chapter information is lost and set to whatever chapter the book gets opened to. This is a long standing bug that Kobo definitely know about.
There is a work-around. The annotation files are in the directory named "Annotations" within the directory "Digital Editions". If you replace the directory "Annotations" with a file of the same name, the problem will disappear.
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