Bicycle Mechanics - Chain jump noise, only when down shifting and on 2 cogs

I have a tiny annoying noise problem that I'd like to fix if at all possible.. Here goes.

I ride a Specialized Roubaix Comp '06, I stuffed an ultegra 11-23 cassette and derailleur (10 spd), it came with 105 STIs. The problem happen when i downshift onto the 2 middle cogs of the cassette; It does a little jump once every revolution of the cassette. Looking at it in slow motion, I can see one of the smaller cog's teeth grabbing the side of the chain and lifting it, then the chain comes back down, making the noise that annoys me most. This only happen on two cogs as said before, and only when downshifting -- When I upshift onto them, the noise's gone. Also, a tiny nudge of the STI gets rid of the problem.

Here's what I (And my LBS wrench) tried so far: straightened the drop out, changed the cable and sleeves, and we tried a new cassette and chain on there. None of those things helped (same noise issue, same cogs). We've also tried the rear wheel on another bike and it still did it on there. After an hour of messing about, the wrench said it was a trademark of Shimano in general. I am not giving up, however.

What could possibly cause this? Please help.

Did you adjust the indexing on the rear der? The only common denominator in your scenario is the derailleur. Get another opinion too. Each mechanic knows something different.

You say he straightened the dropouts, did he straighten the der. hanger?

Did you adjust the indexing on the rear der? The only common denominator in your scenario is the derailleur. Get another opinion too. Each mechanic knows something different.

You say he straightened the dropouts, did he straighten the der. hanger?
Actually, hanger is what I meant yeah. :o Adjusting-wise; I've done my best on my own and everything shift sharply and squarely but those two cogs (and only when downshifting) -- Adjusting the indexing for those two cogs throws off all the other. The wrench came to the same conclusion as well as far as adjustment goes.

I had the intention to hit another LBS and get their opinion. I posted this here to know if this is common occurrence or if it should get looked at?

I realize this is hard to troubleshoot from afar so I understand the lack of response. But I have a quick question (If anyone goes far enough in this post to read this. :D) is the 105 rear STI supposed to have some sort of trimming on the downshift? That's really what this look like. When I downshift at first it's usually a tad bit too far down toward the smaller cog still -- If I then nudge the lever a little it places itself properly. Is that normal? Hoping to be clear enough. :o