Funnily enough I'm having a similar issue... except I've ONLY got the titles for Yuri and Karol (admittedly two of the toughest to complete)...
I set myself back in my efforts to get the titles because I initially modified my first playthrough near the end using a much earlier version of Homura's editor that I managed to scrounge up... and it changed all sorts of things I didn't want it to, including adding all the glitchy titles and stuff, thus buggering up my actual title collection (I'd got most of the tough ones legitimately). Failed again when I tried carrying titles over to my second playthrough, incorrect in my assumption that it might fix what went wrong.
I got Nova's editor while partway through my second playthrough... and I'm now on my 3rd.
I didn't bother carrying over the titles this time, opting instead to try and add them with Nova's editor... BUT it only worked for Yuri and Karol. Estelle, Rita, Judith, Repede and Raven are all presently lacking their titles despite my trying to edit them in three times now... and I can't afford to get them all manually this playthrough as I'm doing my speed-run (and I've already missed the first event for Estelle's teacher title dealie).
I'm absolutely dreading doing a 4th run... -_-; This game is consuming my life...
Just 3 achievements left to get:
The Speed Run....
The 100% Completion...
And those damned titles.