IMO, a combination of things...
There is obviously the fact that in Oakland he played mostly press man coverage, which he was great at. In Philly, he played a lot of zone and seemed to be out of position a lot. In press coverage Namdi was great at reading a players movement and putting himself in position to take the route away. In zone, it is a little different. One thing about Nnamdi is that he is not really a big time ball-hawk. He had one year where he get a lot of picks, but for the most part, going for picks is not really his game. There is an art in baiting quartertbacks into making throws and then making them pay, and Nnamdi isnt great at it, he just takes the route away and makes it very obvious that his man isnt open. Then theres also just the fact that the Eagles were a mess. He was probably frustrated and was not playing very inspired. Of course he played for years in oakland and never let the losing affect his play, but its different when you sign a big contract to go to a contender (he probaly coulda gotten more money elsewhere but wanted to go play for the "dream team") and the whole team is playing horrible.
I dont know if he will ever be his old self, but I dont really see why not. His game was never about speed, it was about using his length, strength, smarts and technical skills to shut down receivers. Hes in his early 30s, and isnt too slow to hold up in man coverage. All signs say he signs w the Niners, and if they can get anything close to what he was in Oakland, it could be scary. The 49ers have the pieces in place to build one of the best defenses in NFL history, and to me they are a shutdown corner and a playmaking safety away from being flat out ridiculous on defense. The loss of Goldson hurts, but they have plenty of guys who can run and hit on the defense, what they need is to improve their coverage. Goldson was good in coverage, but it was his forte.