Because after the initial positive test of Boomer (which Baltar hides to save his neck), and Baltar later discovering that each sample will take ~11 hours to test, he fixes the cylon detector to give everyone a pass.
The functioning Cylon detector created by Baltar confirms that Sharon
Valerii is indeed a Cylon, a fact that Baltar hides from Valerii,
fearing what her Cylon persona would do were he to tell her (TRS:
"Flesh and Bone"). After discovering that it would be easier for him
to make all the results "green," Baltar alters the device to mimic
this method of thinking (TRS: "Tigh Me Up, Tigh Me Down"). However,
after Sharon Valerii shoots Commander Adama, everyone believes the
Cylon detector to be a failure, thinking that it did not pick up her
Cylon nature (TRS: "Resistance", "He That Believeth In Me").