Whilst they are indeed different systems it's not too hard to setup a test that cancels out the differences. A reasonably evenly lit surface correctly exposed surface should yield the same results in auto and manual. Whilst the values maybe wrong they should at least be consistently wrong.

Still I have to agree (again) with Federico, 2500K is very low, well into candelight. Unless the lamps are on dimmers or the building has a wiring fault something is wrong here.

Hi Bob
that's precisely the point I am making: they values might be wrong, but should be consistently wrong

the value I get from auto (around 3400) seems much more correct to my eyes (at least)

my EX1r is still under warranty so I am not worried, but just trying to understand if there's a fault or not

The best thing you can do to establish whether the camera is faulty or not is to do a proper manual white balance and then look at the output on a waveform monitor and look at the RGB parade or vectorscope. On a vectorscope the white should just be a spot right in the center of the scope or on RGB parade the white R, G and B levels should be equal.

This eliminates the monitor or other variables and is more accurate than judging by eye

You could record a clips and look at it in your edit software.

If you lack the gear or experience to do what Alister is suggesting take the camera to a large Sony dealership in London and do a comparison between your camera and another one.
Maybe as others have speculated you're doing it wrong, hopefully someone in the shop will set your right.
Maybe your camera does have some strange fault, again a trip to the shop would resolve that.
Short of one of us having your camera in our hands all we can do is speculate.

I didn't read through this whole thread, but I thought I'd add this:

1) Don't forget to set the camera to Auto Iris before you hit the white balance button. This has tripped me up a few times.

2) Make sure that the light falling on your subject is the same EXACT light that's on your white card. Sometimes you have tungsten lights coming from fixtures in the ceiling, while you have daylight pouring in through windows - all happening in the same scene. This can make white balancing very tricky. (In this situation I've learned to either close the blinds to eliminate the daylight or set up some portable tungsten lights to over power the daylight coming in the windows)

Just my $0.02. Sorry if this has already been covered....

that's a good idea, but believe it or not it's quite tricky to find a shop in London that sells the EX1r
mine, I had to go well out of town to buy it and I already contacted the shop, who very unhelpfully responded they weren't sure, and want to charge me £125+VAT just to have it checked!!

any fellow DVInfo member in Central London can be around for a quick test?