I also have this problem.
I still have not found where the problem is coming from.
But i did find a little work-around.
After copying the books to the reader, go to the reader within the Calibre windows (just right of the Library button).
In that window, you can see the books and there tags.
If you find a book without a tag, just double click on the part were the tag should be. Now you can add the tags and series description you want.
This stays in the reader.
But i hope that a definitive fix can be made, because it is not easy if you have to do a lot of books this way.