IIRC - the note may have been left out in the open by LE after going through her room.... remember LE was working under the impression that MM was suicidal....
I guess it comes down to the credibility of the LE in question. Here is part of his official statement concerning Maura's dorm.
LT. John Scarinza: "By Monday morning, Feb. 9th Maura had packed up all her belongings in her dorm room at U-Mass, putting everything neatly in boxes and putting all the boxes on her bed along with a personal note she had recently received from her boyfriend. She went on the Internet and looked up directions and overnight accommodations in the Bartlett, NH area as well as Burlington, VT area. She withdrew most of her money from her personal bank account. She sent e-mails to her supervisor at work as well as a college professor saying she would be absent from work and school for a week due to a death in the family."
The note as I understand it was actually just a part of a longer note that Maura's boyfriend had written her and the subject manner of the note had to do with him cheating on her.
I will once again say that as long as this LT is on the up and up and is feeding the public accurate information, then I do believe that he and his fellow investigators discovered even more information (like from Maura's computer) that led them to their suicide theory.
The only reason, they would've somewhat backed down from that theory (which they did so after taking heat from it) would not be because they no longer believe it, but rather that public perception from taking a strong stance like that would mean they would have to put up or shut up (about the sucide theory) and I don't think they want to be pinned into that kind of corner, until they uncovered other evidence ... which has been a long long process still in the making.
We heard about the directions and mapquest from Maura's computer, but that is just the kind of information the police didn't mind if the public found out about. It is very likely there were other things the police discovered that they have never publiclly released or for that matter even possibly, let the family of Maura in on.
And this is all just my opinion, I am merely taking a guess, but as I see it, the evidence is really starting to add up that maura may have been suicidal or having thoughts of suicide.