I've heard many times that saying birchas hatorah is most likely from the torah (as apposed to mi-dirabanan). How could we not know? If it's from the torah, then it's from the torah!
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The Gemarah in Brachos 21a and again in Brachos 48b brings a Posuk as its source and many Rishonim learn it as an actual Torah source but Ramban (Nachmanides) maintains (Hasagos Ramban LeSefer HaMitzvos, Shikchas HaEsin 15) that from the fact that Rambam (Maimonides) left it out from his count of the mitzvos means that Rambam must hold that the verses quoted are just asmachtos (instances of attributions of a rabbinic law to a Torah text), and really it is just like all other Birchos Hamitzvos (blessings made before fulfilling certain commandments). Aruch HaShulchan (OC 47-2) argues with Ramban and maintains that Rambam did hold it was a Torah-based commandment, however it is included in the mitzvah of Talmud Torah, learning Torah. If Ramban is correct regarding Rambam's position, Rambam is a daas yahid (lone opinion) on this issue. It seems that the exact tradition whether it was midioraisa (a Torah based obligation) or not was not explicitly taught and the Rishonim on each side have their reasoning as to why they hold what they do. There are many instances of lost Mesorah which results in a later argument.
Not necessarily. There are indeed various halachos where there is a dispute whether they are Biblical or Rabbinic obligations. One example that I can think of, offhand, is tevilas kelim (immersing dishes), about which Pri Chadash (Yoreh De'ah 120:1) cites variant opinions as to its source.
How did such a dispute develop? Same as any other machlokes. Details of halachah have been forgotten at various times in history (as far back as after Moshe's passing - Temurah 15b ff), and in trying to reconstruct them, different Rabbis will have different opinions. (There is a great book, The Dynamics of Dispute: The Making of Machlokess in Talmudic Times, by Zvi Lampel (Judaica Press, 1991), that discusses this topic from many different angles.)