Colorsync calibration problems

I have a problem with colour mismatch between Photoshop CS6 and OSX native apps such as Mail and Preview. If I calibrate my monitor (a Dell U2711) using a hardware calibrator (colormunki) and set this as the monitor profile in System Prefs the colours of images don't match when viewed in Photoshop and Preview*. They are way off, perticularly in saturation and shadows.

However if I do a manual calibration by eyeball alone with Apple's built in calibration software and use this profile in System Pref, then the colours match much more closely. Not perfect but better than using the hardware calibrator.

Now, I don't know what is going on here because the reverse should be true. I also get duplicate colour profiels in the Display Profile list in Systems Prefs.

Something seems screwy.

(* Photoshop is set up using the defauls European Prepress 3 settings and when I save out a Jepg to view in Preview for example I embed the profile. The monitor itself is set to sRGB colour space, which is what the Euro preset is also)