I also have the same problem.
If I do a F&R for say <div> to <p> for a whole chapter of text. Every thing changes ok, but, if I click on the code page all the <div> come back.
If I do a F&R again everything changes and stays changed. and I can keep changing things until I finish that chapter.
If I start on another chapter with F&R it has to be done twice again for the first one.
Very strange. I know now that I have to do it twice, so I just do it.
Ah, the mysteries of computers.