This is because the sun doesn't use a timex, it has its own path which is not as "precise" as our timepieces.
The Earth doesn't go in a nice circle around the sun, it travels in an ellipse (Kepler's 1st law of Planetary Motion). When the Earth is closer to the sun (in our winter) it travels faster. When it is farther away (in our summer) it travels slower. The cause of this is gravity-similar to when you put a coin down a march of dimes wishing well at the zoo. It can be illustrated using Kepler's 2nd Law of Planetary Motion. The end result is that our watches are off from the sun's "motion".
Although the Sun's time is relatively close to the time on our watches, Kepler's laws have an halachic ramification for kidush hachodesh. Rosh Hashana 24b:-25a Two witnesses said they saw the old moon in the morning and the light of the new moon in the evening. Rabbi Yochanan ben Nuri tossed them as fabricators since the calculation was that a new moon is covered for 24 hours. Rabban Gamliel accepted them since he had a mesorah that the moon's movement fluctuates. (The amora Rabbi Yochanan brought a supporting pasuk- "Shemesh yada mevo'o"- but not the yareach).