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I was watching the original trilogy recently as I often do, and I noticed something, as I often do. I have what might be called the DVD Special Edition, I know it has Special Edition features, but were some more added for the Trilogy Boxed Set release on DVD?

Anyway in the redone scene where Vader gets a call from Palpatine, the dialogue was changed so Palpatine says something like, "We have learned the rebel who destroyed the Death Star was the son of Anakin Skywalker.." Vader is in disbelief at first but eventually believes it to be true after searching his feelings. But up to that point, he has already pointed out he was searching for "Young Skywalker". From the beginning crawl where it points out Vader is obsessed with finding Skywalker to the scene on his Super Star Destroyer where he sees the video from Hoth and states, "The Rebels are there and Skywalker is with them.."

So here's my question. Does Vader already know that was his son he chased on the Death Star? Is he secretly already looking for his son behind ol' Palpatine's back? Then he acts shocked when his master tells him it's his son? I think it could be, I think Vader is strong enough with the Force that he "felt" his son long before Palpatine, and now he is getting the ball rolling to unite with Luke so they can rule the galaxy together.

Vader basically learned about Luke during the time period between EP IV-V. Vader did not know it was Luke in EP IV. Vader says "This force is strong with this one" during the trench run. Remember, Anakin Skywalker is a name Vader has forgotton

Ok, I have some more evidence. Here is what we have so far:

1. Between Episode IV and V Vader learned the Death Star was blown up by a "Skywalker", whether he knew right off the bat it was a relative or not we don't know. But the opening crawl indicates he was "obsessed" with finding Skywalker at the beginning.

2. When the Hoth base is discovered by the probe droid, Vader, from lightyears away in his Star Destroyer, says "That is the system. And l'm sure Skywalker is with them".

3. In RoTJ, Vader goes to see his master for orders and they have this conversation:
Darth Vader: My son is with them.
The Emperor: Are you sure?
Darth Vader: I have *felt* him, my master.
The Emperor: Strange that I have not. I wonder if your feelings on this matter are clear, Lord Vader.
Darth Vader: They are clear, my master.

This strengthens my belief that, at least from the start of Episode V, Vader was aware a Skywalker was alive, even though he seems shocked by Palpatine's statement that the son of Skywalker lives. This opens the possibility that Vader had his own agenda to find his son from a much earlier point, either to defeat the Emperor and rule as father and son or perhaps even to protect him from his master.

Like you said: Vader already knew of Luke's existence well before Palpatine brought it up. Therefore, the only logical conclusion is that Vader was feigning ignorance during their transmitted conversation in ESB.

Of course Vader had his own agenda. I think that point was clear a long long time ago. He even said it to Luke after chopping off his hand: "You can destroy the Emperor, he has foreseen this. Join me and together we can rule the galaxy as father and son."
Vader clearly had a double agenda: bump Palpy and have his son as apprentice (in true Sith fashion) or, if unwilling, kill Skywalker and continue his submissive apprentice-status which he apparently can't shake by himself. ("You don't know the power of the dark side. I must obey my master.".