1) I suspect this could be because the Phosphors used in the SMT device are different to the T1 LED. Possibly a more recent blend or maybe just plain different - this would alter the energy distribution that the CMOS sees - possibly in a way more favorable to the device's own response curve. Google - color temperature and spectral energy distribution and color rendering.
2) You don't mention how you are powering the LED... - you can also see effects due to the drive paramaters of the LED - if not pure, continuous dc. LEDs respond so quickly they can defeat the sensitivity of conventional film - a phenomena known as reciprocity. If you have an LED driver with a non-continuous repsonse this will impact exposure times - I am guessing - the CCD / CMOS has a time-dependent response too - which could in turn be impacted by the shape and slew rate of the LED driver curent waveform.
3) Finally, the size of the illuminating source in any system impacts the shadow quality - and eventually the perceived sharpness - of the image. ...The reason why news anchors always have softlights on them - to hide the wrinkles... and why shadows are harder at dawn and dusk - the source size. Bigger or smaller the source (meaning energy per square mm heading in a particular direction in your case...) the softer or harder the image. ...In short, you don't have a shadow on a cloudy day - vampires aside. The shadow quality will influence the displayed / percieved contrast of your system.
4) Going to theoretical (as data says...) I believe there are some centuries-old illumination techniques specific to microscopy that play with light source image and position relative to the objective - names escape me right now... Puts the light on the thing you are looking at - not the thing you are looking though. Your new SMT source probably has a 120 degree Lambertian light distribution -Google it - your old one probably a 60 degree distribution. End result - the light is coupled through the thing you are imaging in a different way reletive to the objective compared to the original system. End result a radomly better or worse image depnding on what you are looking at and where the source is located relative to it.
>>Smart money says its the die / phosphor combination - SMT white light is constantly moving forward... improving from a human preception point of view over the past few years.
Jon Connell, MIES, MIEEE
Brooklyn, NY