Evidently, from the flimsiness of available information in material in related questions here and on the BG wiki page on the Cylon detector, as well as from having recently watched these episodes and having been left with the same questions, it appears that:
- Baltar is very frightened in general and is surprised by the result.
- Baltar is caught in a web of guilt and his own lies, and has a nutty weaselly behavior pattern where he tends to make very unwise short-term decisions including inventing regrettable lies on the spur of the moment.
- Baltar's thinking is severely skewed by visions of Messenger Six, including specifically being afraid that he needs to appease her.
The wiki asserts that he was afraid that if he told the first positive subject she was a Cylon, she might kill him, but that only covers why he'd cover it up at that moment. It doesn't explain why he didn't then go tell, say, Adama. It also says nothing about the second case that your question asks about.
My feeling is that even the first case is a somewhat mysterious weak point in the plot, but that it's covered by Baltar's irrational fear for himself combined with Messenger Six's bullying, making him afraid enough to cowardly prefer pretending the detector is failing, to having to out anyone. That is consistent with many other cowardly short-term evasions that Baltar chooses in other stressful situations. He's crazy that way.
Having lied in the first case, revealing the second case might open him up to future investigation if/when the first Cylon were discovered. Baltar has a tendency to try to double-down on his lies rather than admit to an earlier one. Again it doesn't make a lot of sense, except that Baltar is crazy from fear, lies, guilt, and Cylon psychological torture.