I don't see this behavior, which means that what I am doing isn't the same thing you are doing.
You say you have a column for read/unread information. Is this a calibre Yes/No column? If so, is CC configured to sync that column with CC's Read information? If it is not a yes/no column then what kind of column is it?
If your column and CC's read information are not synced, which line are you tapping in the grouping drawer?
Here are some screen captures of what I see. This first one shows the library with nothing selected in the grouping drawer. You see Read, Not Read, and not marked books.
The next one shows the grouping drawer open on the Read information.
I tapped the "<<>>" line (which means neither read nor not read) and the library changed to the following. Note that both the Read and Not Read books are no longer listed.
The next capture shows the grouping drawer with "Yes" tapped.
And the library after tapping Yes. It shows only the Read book.
And the library after tapping No.
Does any of the above trigger some ideas?
A CC debug log might help determine what is happening. To send me one, go to CC's settings, scroll to the bottom, and select Send a debug log to MultiPie. Please erase the multipie.co.uk email address; this avoids taking my son's time when I am handling the question.