You are in good company! The Chasam Sofer writes (Chidushei Yevamos 22a, among other places) that he searched for a source for this Halachah everywhere and was unsuccessful in finding one.

The Rambam in his commentary on Mishnah in Demai (6:10) writes that "the religion separates between a non-Jewish father and his Jewish son," but even this ambiguous explanation cannot explain all the Halachos of Ger she'Nisgayer.

Dov Zupnik

From Rashi in Bava Kama 88a DH Ger Ein Lo Chayas, it seems that the Mekor might be "Zirmas Susim Zirmasam," (i.e. that once a person is Megayer, we cannot consider a Nochri to be of the same family - even a mother and child).

See also Meshech Chochmah, in va'Eschanan (Devarim 5:27).

M. Kornfeld

[The Meshech Chochmah there cites the Chasam Sofer, and then suggests a brilliant source for the Halachah. The source for the Halachah (with regard to familial relations) is the verse, following Matan Torah, in which Hash-m tells the Jews "return to your tents" (i.e., to your wives), even though many of them must have been married to women that were not permitted to Jews after Matan Torah (such as Amram and Yocheved).]

According to the Meshech Chochmah, when the Torah says that those who left Egypt cried after Matan Torah because they became prohibited in the Arayos (Bamidbar 11:10 and Rashi, from Yoma 75a), it must mean that they were crying over future Shiduchim, who were not yet born. Those Arayos who they left Egypt with, though, were permitted to them as "Katan she'Nolad." This does not conform with the simple reading of the Sifri there, #90, that says that they were married to their sisters etc., and were upset when Moshe told them to separate from Arayos.

As for why they were not actually judged as Katan she'Nolad when the Torah was given (if we do accept the Sifri at face value, and do not accept the Meshech Chochmah's explanation), the MAHARAL addresses this (Bereishis 46:10). He explains that Gerim who were converted "by force" (Kafah Aleihem Har k'Gigis) do not have the rule of Katan she'Nolad. It seems that he means to differentiate between the Geirus of the entire nation, as one unit, and the Geirus of a single person who separates himself from his own nation to join Klal Yisrael. (Or maybe he means that one who does what he must do is not separating himself from his past at all. Only a Ger who changes from the norm by making himself a member of a different nation can be called a newborn.)

As for a Remez that Ger is k'Katan she'Nolad, perhaps the very word "Ger" contains such a Remez. Rabeinu Bachye explains in a number of places (Bereishis 31:39, Shemos 22:20, Vayikra 24:20) that the word comes from "Gargir," meaning a single seed, or grape (Yeshayah 17:6), which is completely separated from rest of the plant. A Ger is cut off from his past and alone.

Thanks for the Mar'eh Makom!

-Mordecai Kornfeld