The "disk" episode investigations were very early in the series and demonstrate the growing investigation capabilities of Olivia Dunham. She was "assigned" to the group, and it could be believed that she was a little put out by it. The mere name "Fringe" could have been mocked by her other FBI compatriots before her transfer. Today she is fierce, self-motivated, and determined. Earlier, she was still being called "Liason" by Broyles and she was unsure of her true investigative standing in the Fringe Division.
I think Nina from Massive Dynamic (MD), knowing the knowledge that Dr. Bishop possessed, and the power Olivia was capable of, used her relationship with Broyles to temper the early investigations. It wasn't revealed until later that MD was deciphering some data from the disks; I think this came after Olivia earned her cortexiphan stripes by defusing the Jones bomb. At that point, I think Nina allowed Broyles to let Olivia determine where and with whom an investigation would lead.