The simple explanation is that the main Mitzvah of reading the Megilah is during the day. Tosfos brings two proofs that this is so. Accordingly, the Berachah of Zman is said not only the first time the Mitzvah is done (at night), but also before the primary time that the Rabanan decreed that the Megilah should be read, which is during the day. There are those who argue that it is not possible that Shehecheyanu should be said twice for the same Mitzvah, regardless if the second time is the primary time the Mitzvah must be performed. The Pnei Yehoshua seems to be bothered by this, and gives an alternate explanation (unlike Tosfos). He explains that the Shehecheyanu said at night is not for the Mitzvah of reading the Megilah, but rather for the beginning of the "Yom Tov" of Purim. The Shehecheyanu during the day is for the Mitzvah of Megilah. However, it should be noted that many Rishonim (Rashba, Ritva, etc.) accepted the logic presented by Tosfos.

All the best,

Yaakov Montrose