If you're using Sony's software to load the books, you also have to tell that to use the new font.
See Appendix E in Valloric's Guide to changing fonts v1.2
https://www.mobileread.com/forums/showthread.php?t=28447
edit**melrowgo upon rereading your question, it looks like you've already done the above.
To test, you could try dragging a book directly onto the reader with Windows Explorer or adding it through Calibre. That way, the reader will be forced to paginate the book. If this works properly, then I'd try replacing the font Reader software is using again.
Good luck!
dordale