Bicycle Mechanics - help! mystery shifting problem

A couple of weeks ago I got a new frame for my road bike and switched all of the parts from my old frame to the new one. While I was at it, I put on a new chain and cassette. Everything works perfectly except for one thing: I have a mysterious problem with my rear derailleur/cassette/lordknowswhat. These same exact parts were working perfectly on my old frame (except for the new chain and cassette, of course). I am using a 9 speed sram chain with a 9 speed campagnolo cassette (the same combination I've used for several years without a problem).

Here's what's going on: It makes a clicky/grindy sound when I pedal, and the rear shifting is slow and loud. The sound is coming from the area of the cassette, and it is louder and the shifting is slower in the smaller cogs and when I am pedaling hard.

Here's what I have done so far: I have adjusted the derailleur so that it shifted almost perfectly while it was in the stand. On the test ride it shifted poorly. I must have spent 30 minutes riding up and down my street and making small adjustments to try to get it to shift right. Needless to say, the issue persisted. I went down to my LBS to see if they knew what was wrong. They adjusted the derailleur again and had the same issue I had: on the test ride it just wouldn't shift right. Two different people at the shop worked on it. I finally got it adjusted to where it's pretty functional, but its still annoying.

Here's what I'm wondering: could this be a dropout alignment issue? If it is, it is not so misaligned that it's obvious when you look at it. What else could it possibly be?

LBS can check hanger alignment easy enough.

Did you check the alignment of the hanger both laterally and in the fore-aft direction? I would hope the shop would have slapped a DAG-1 on there to check alignment. I never do it by eye as that's mislead me before and it's not exactly time-consuming to check with the tool.
Could also be a minute crack in the hanger-I've had a situation like yours occur once and that turned out to be the culprit on a particularly flimsy alu hanger.
Assuming your cable tension is proper the hanger becomes the most likely suspect beyond shots in the dark like a loose cassette.

Hmm. If it is working perfectly on the stand, but crap when you ride, is the frame buggered? It would flex badly, wrecking any adjustment, perticularly when pedalling hard. New frame, could be a dud.

There are 2 essential tools for checking the frame alignment and hanger alignment-- did the shop use those? The frame tool looks like a giant (24 inch) arc with a pointer in the middle. And the hanger tool threads in where the derailier goes, so you have to take off the rear deralier to use it.

There are 2 essential tools for checking the frame alignment and hanger alignment-- did the shop use those? The frame tool looks like a giant (24 inch) arc with a pointer in the middle. And the hanger tool threads in where the derailier goes, so you have to take off the rear deralier to use it.

I'm going to take it back to the LBS tomorrow and insist that they check the alignment. The other day when I took it in they dismissed my idea that it might be a misaligned dropout or bent hanger because it was a new frame.

is the chain the same size? or the same brand and type? and does the chain fit to the new cog?

Here's what the problem was: The derailleur itself was bent. I don't know how it happened. Of course, I guess all kinds of things can happen when you leave your bike locked up at a college campus all day.