In the BSG Miniseries we see a entire squadron of Vipers be disabled by the CNP so, why wasn't the raptor also disabled?
I can't find a script online to give a direct quote, so this is going to be a paraphrase. For reference, the scene starts at 52 minutes.
At the start of the scene when they're approaching the Cylon raiders, the CAG at the time tells Boomer to "back way off" and the Vipers will "take it from here."
Boomer stops her Raptor the Viper squadron flies ahead. It looks like the Vipers aren't even in visual range anymore. My assumption is that this put the Raptor out of range of the Cylon interference.