One idea would be to eliminate the extra save files and see if that helps matters. Another method would be to see if playing through the game twice makes a difference. Beat it once? See if the final trophy pops and then revisit all the stages for cleanup.
A patch concerning this matter might be the best thing though. Of course that would all depend on if Idol Minds is knowledgeable about any of the game's issues and working to fix them up.
Well, at least one thing to keep in mind is that not all skill points are singled out for trophies. There are some trophies unlocked right away after a skill point is reached. Others meanwhile are separated from the group as a handful of them are just part of the whole lot. Eventually you should be able to unlock all 30 skill points. Those ones such as the one that sees you swinging without touching the ground is not intended for a trophy by itself. Others like defeating the queen with only a hammer are based around a trophy.
If the ones that you know should get a trophy are not working out, then that's when you know there's a problem. Just keep in mind that not all skill points are tied to a specific trophy.
