Philosophaie,
There is absolutely no reason to expect that Earth's perihelion will occur when the longitude of the Sun is equal to zero. They are very different things. Perihelion passage occurs once per anomalistic year, when the Earth is closest to the Sun. The longitude of the Sun equaling zero occurs once per tropical year, when the Sun as viewed from the Earth crosses the Earth's equatorial plane heading northward.
Note well: perihelion passage occurs once per anomalistic year while longitude of the Sun equalling zero occurs once per [/b]tropical[/b] year. They don't even occur at the same frequency. If they happen to coincide during some year, they will not coincide the next.
I've already introduced the concepts of the anomalistic year and the tropical year. There is one more definition of a "year": The time it takes the Earth to complete one orbit around the Sun with respect to an inertial reference frame, or to use a slightly outdated terminology, with respect to the fixed stars. This is the sidereal year.
Our calendar is based on the tropical year because we want the calendar to by in synch with seasons. The Earth's axial tilt (technically, the obliquity of the ecliptic) is what determines the seasons. The distant stars (the sidereal year) obviously have no impact on the seasons. Less obviously, the proximity of the Earth to the Sun (the anomalistic year) plays a much lesser role in determining climate than does the axial tilt.
That proximity to the Sun has only a secondary effect on climate would not be true if the Earth's axial tilt was much smaller than it is and the eccentricity of the Earth's orbit was much larger. Playing "what-if", if the axial tilt was near zero but the eccentricity remained small (~0.0167), the weather would be much more uniform year-round because that small eccentricity results in only a 7% variation in radiation intensity over the course of a year. If the eccentricity was also significantly greater, the "what-if" Earth would once again have seasons, but in this case the seasons would be dictated by the anomalistic year.
Back to the real world. Why are there three different "years"? First, the sidereal year versus the anomalistic year. First a bit on Keplerian orbits and orbital elements. Orbital elements comprise the semi-major axis of the orbit, the orbit's eccentricity, three angles that describe the shape and orientation of the orbit, plus the true (or mean or eccentric) anomaly. Keplerian orbits occur only in fiction -- and in introductory physics classes. The Earth and Sun would orbit their center of mass in a Keplerian orbit if the only objects in the universe were the Earth and the Sun, and if Newton's law of gravity perfectly described reality, and if both had spherical mass distributions.
In a true Keplerian orbit, only one of the six orbital elements changes with time: the anomaly. The remaining five elements are constant. The anomalistic year and the sidereal year would be equal to one another in this fictional universe. Our solar system has multiple planets and Newton's law of gravitation is only approximately correct. Those other planets, particularly Jupiter, perturb the Earth's orbit around the Sun. The Earth's perihelion passage does not occur at exactly the same place every year with respect to the fixed stars. It instead precesses (called anomalistic precession) a tiny bit. That Newton's law of gravity is not quite correct adds a tiny bit to this precession. The end result: The anomalistic year is about 4.7039 minutes longer than the sidereal year.
The tropical year differs from the sidereal year because the Earth isn't a perfect sphere. The Earth has an equatorial bulge because the Earth is rotating about its axis. The Moon, the Sun, and the other planets "grab" this bulge gravitationally, resulting in a torque on the Earth. The Earth wobbles a bit (called precession of the equinoxes). The Earth's rotation axis in turn rotates about another axis, completing a revolution in about 26,000 years. The end result: The tropical year is about 20.3628 minutes shorter than the sidereal year.