In the beginning of Interstellar, the mysterious behavior of gravity is attributed to Cooper's discovery of the secret NASA base that leads him to becoming the lead astronaut. When they first find out about how he found out about the base they are very interested in investigating it further. But it seems like they never really follow through - I would expect a full on occupation and quarantining (and thus discovery of Cooper in the bookshelf) of the house so they could get to the bottom of it. Instead, it takes something like 30 odd years before the cooper's daughter begins the arduous task of translating the atemporal medium. How come Cooper couldn't simply get the attention of the NASA guys in the very beginning when he's in his super time cube?
According to me there are few points which makes NASA not to bother more about how Cooper got the NASA co-ordinates
When Cooper arrive at NASA , the NASA scientists are curious to know how Cooper got the co-ordinates because they want to confirm that the co-ordinates are not leaked to the outside world and cooper is not an agent sent by some other organisation.
The NASA scientists don't know who placed the wormhole near Saturn, but they say that whoever has placed it has done it for Earth's good and they are least bothered about knowing who placed it because it's impossible.
When Cooper tells that some mysterious behavior of gravity gave him the co-ordinates, all the scientists think that the same power or the intellect that has kept the wormhole has somehow directed Cooper to come to NASA. So they all think that the intellect who kept the wormhole wants Cooper to be with them for some good purpose even they don't know.
I also think that only Cooper could send the messages from the three dimensional representation of the time. So even if NASA would have come to investigate Murphy's room they would have found nothing but just falling books and some gravitational anomaly but they couldn't find Cooper (this is according to me, may be some others have other point of view also).
So NASA thought the mysterious behavior of gravity as a help from the "someone" who kept the wormhole near Saturn, so NASA chose Cooper to be the pilot of the voyage. Until then they had no such plans of sending a retired NASA pilot on the mission.
The anomaly present is very minor. It consists of a few lines of gravity only a foot long, three feet wide and maybe six feet tall. Just enough for dust/dirt to pile up. No mention of how long it lasted. The next anomaly appears just a few days later, centralized around Murphys watch. That sticks around for 25 years atleast, but you'd have to know it's an effect of gravity (somehow, cause gravity doesn't work like that) and not just a broken watch. Even if Super secret Nasa investigated, there doesn't seem to be much that could be learned.
And thus discovery of Cooper in the bookshelf.
Tesseract Coop was not physically in the Bookshelf in three dimensional space. That would place him in a wall, another room, or floating outside the house. He's in another dimension(s). The Tesseract is a construct of space just meant for Coop to be able to understand, as he is primitive compared to They. He's floating in fifth dimensional space. Even then, modern day humans had neither the understanding or equipment to detect someone in that space.
Furthermore, relative to modern humans, Coop only affected a few minor periods of time. Nasa only first knew of the anomalies for a few days at most. The three major events, the coordinates, the STAY and the watch, happen within days of each other. The window of observation would have been way to small for Nasa to learn anything.