One thing to be aware of, there can be a loss of shadow detail in the digital printing systems from E6 Slides, I only shoot E6 in 35mm and have had a ton of prints made from various slides and the shadow detail is lacking in many of them, due to the digital scanning process and exposure on normal print papers, it seems to give a bit of a softer look as opposed to the C41 prints my wife has done.
On your reprints, did you give them a print to match the colors from? Even though we are in the age of so called digital perfection, the person printing the picture is in charge of the color corrections and such, and I can almost guarantee you, two sepreate individuals sitting down to the machine are going to make different choices on what they feel color balance is, hence you will receive prints at different times with different color balance, when I was shooting weddings, I always made sure that if I thought I was going to require prints in the future, that I either kept a copy of the prints for myself, or I at least wrote down the settings that are printed on the back of the print so we would have a base for starting out, when the prints needed to be redone.
Another thing to keep in mind, many of even the pro labs have become lax in keeping their machines calibrated in the digital age, the lab I worked at we found out, that we needed to calibrate the machine at least a couple of times a day, and if we changed emulsion numbers on the papaer we had to recalibrate to keep everything in correct calibration.
So there are manythings that can come into play when your doing reprints if the colors are off or different.
Dave