I don't mean to be digging up dead threads but this exactly describes the problems I'm having too.
I've triggered at least two appearances of the shadowy figure that you see right at the beginning of the game but instead of dialogue it just disappears after a second or two. One instance was in the Kelp Forest and another was in or around the Sun Temple, possibly the Veil. I too am now wondering what else I've missed.
I've found this rather sparse wiki on Aquaria detailing hidden scenes but nothing saying what you can expect to find during the normal course of play.
http://strategywiki.org/wiki/Aquaria/Hidden_MemoriesIf someone could fill me in on what I've missed, or tell me how to view the scenes again (I've searched youtube but drawn a blank), that would be great. So far I've been to the starting dungeon, the place that looks like an old castle, the kelp forest and mother nature, the veil and the Sun Temple. I've seen the shadowy figure three times but only had dialogue once, right at the start. Other than that I've not seen or heard anything other than when I find a hidden object, Naija makes one of her comments when exploring a new area or I kill a boss.
I'd really like to know what I'm missing!
I'm running whatever the latest version is on Steam if that helps.
TIA.
EDIT
I've stumbled across a video playthrough of Aquaria. In this video, at the 7 min mark, the exact same appearance of the shadowy figure occurs without dialogue so perhaps this is normal (or a common problem?). Interestingly I don't remember seeing her here but I could be mistaken.
http://www.viddler.com/explore/D-ak-tar/videos/10/