Damn. That sounds confusing as hell :p I really need to make it easier for folks to access main story with just a button.
Although to answer your question, if you're using an old save, try creating a new one. (Usually that fixes a lot of issues.)
Also, can you specify what you mean by "you can't do it"? Is it still grayed out?
The buttons in my game does not access per-chapter basis, instead it goes to a "checking post" and sees your relationship level with the character, then it goes to the chapter where you left off. (Although once it's done, it becomes a per-chapter basis)
I know. I need to code it better.