I always got the impression that Janeway wasn't interested. Even when they were on the planet with no expectation of leaving, she wasn't that interested. Also, it's not uncommon for people who have known each other for years to suddenly shift gear into a romantic relationship. I know a few couples in my own small circle of friends who have done this.
Oh she was interested alright. I saw it and not just on New Earth. You could sense the sexual tension from across the bridge. It's a natural thing I mean...It's Chakotay....