I just rewatched the miniseries last night for fun.
interesing note, I finally know who Caprica 6 was speaking to in the scene where she tells Gauis that she has to meet someone and says it's about time you showed up.
This scene works in reverse and is later recapped on the galactica when both of them are talking about the cylon scanner in CIC.
The person is Aaron Doral.
He had access to the galactica as a PR speaker for the museum. They purposefully go out of their way to tell the viewers how he was able to roam the hallways free to do what he wanted.
Then the flashback to when 6 enters Baltar's house. In her purse/case was the cylon detector.
She was delivering it to Doral to install on the dradis while he was able to roam free as the PR guy.
So there is your answer.
Doral put the device in CIC when the galactica was in the middle of decommissining and no one was looking.