User blog comment:The Milkman/Extended Expectations, Part II/@comment-1441235-20120629062602/@comment-1221773-20120629163330

According the description of the Salarian First Fleet War Asset, the salarians used the Normandy's stealth technology and Normandy SR-2's Reaper IFF to develop stealth dreadnoughts, and the Reapers haven't yet cracked their countermeasures. If the IFF still works for the salarians, it still works for the Normandy SR-2.

As for the Search and Rescue minigame, the apparent contradiction may be the result of 1) the scanning pulse is something that the Reapers can trace to its source, like with radar, or 2) the minigame, as such, simply doesn't take considerations like the Normandy having stealth systems and a Reaper IFF into account.