I should preface this by saying I did search, and while some come close I didn't see this particular issue:

I replaced a dura-ace 7800 11x23 cassette with another 7800 12x25 cassette of about the same wear. Prior to this change the rear shifting was flawless. Have a 2006 Spesh Tarmac, btw.

Now the problem is that when on my 53 chain ring (39-53 rings) I cannot shift to the 25 or 23T cog without the chain skipping or 'wanting' to go down a gear. All this while I have the bike on the trainer -I always test equipment changes for 2-3 days on trainer before going out, exception being tires.

To the best of my ability the derailleur hanger does not appear bent, the pulleys do line up.

I released the tension from the trainer, and it does get better, but not what I'd call acceptable, even after considering chain rub on front derailleur. I also pedaled backwards and it does not down-shift to suggest a tight link.

I've tried to loosen up the tension on the shifter cable (about 2 turns on the knob) but no help either. I suspect my chain is a little too short for this cassette but would like to hear others suggestions before I proceed.

My guess is that your chain is worn. It's often a good idea to replace the chain when you replace the cassette.

^What he said.

+2+.. often the chain needs to be replaced more often than it usually does
get replaced.

put the old chain with the cassette you removed, they wear into each other.

Maybe your bike is trying to tell you something. You are putting unnecessary wear and tear on the drive system by cross-chaining the large chainring and large cog. You can achieve the same ratio with a less-extreme chain angle if you use the smaller chain ring and a more middle-of-the-cassette cog.

+3.

But I also agree with the guy above that you are putting unnecessary wear on the drivetrain by cross chaining.

Good point. However, I'd like to stay on the big ring, reason being I'll be crit racing, and need the taller gearing for sprinting, which is not possible on the small ring. I didn't mean to say I'd be on the 25T, the 23, 21T would be more like it, and only after cornering.

This wasn't a problem with the 11-23 cassette. Why now?

Could the spacing of the cassette be slightly different ? How are the rest of the gears ? I swapped out 1 Campy cassette for a different one and the shifting was off a bit. Had to tweak the adjustment.

Did you remember to install the thin spacer on the inside of the cassette? Failure to do this will move the whole cassette 1mm closer to the spokes and might upset shifting. I have even seen shops that didn't remember this simple detail

Not that I can see with my naked eyes. The rest of the gears work fine.

I installed the spacers the same as they were on the bike that they came from, which again, no issues on that bike. But maybe I'm not understanding your question, what do you mean by the inside of the cassette? where the lock ring goes in? There was no spacer there, as that part is threaded. Again, I think I'm misunderstanding you, apologies in advance.

When you install a Shimano 10 speed cassette, the first thing that goes on is a 1mm thick spacer. After that the rest of the cogs and spacers are installed. Many people do not understand that a 10 speed Shimano cassette is actually 1mm thinner than a 9 speed cassette, thus the spacer is needed. If you didn't install that spacer, your cassette is 1mm closer to the spokes than it was before and your derailleur will no longer be properly adjusted and you will have trouble shifting to your largest cog. If you change your limit screw settings you run the risk of your derailleur hitting the spokes.

Definitely take a look at a new chain, you might also be having problems if your b angle is not adjusted and the RD is not clearing the 25T cog. You might also need to loosen your Low limit screw just the smallest amount.