Out of Order

It’s time to dust off Mesechta Rosh Hashana. The Daf will be finishing with Mesechta Beitza shortly. Someone studying the Daf with an Artscroll Shas will find nothing amiss. However, those who study the Daf with a standard Hebrew Shas will be somewhat perplexed. After all, Mesechta Taanis follows Beitza, not Rosh Hashana. Upon further inspection, he will notice that in his standard Shas, the order is Shekalim, Rosh HaShana, Yoma, Sukka. Being that Yoma discusses Yom Kippur, the order of Rosh Hashana, Yoma, and Sukkah seems to be rather intuitive. Indeed, there have been reports of Maggidei Shiur actually teaching Rosh Hashana for a few days after completing Shekalim before realizing their error. Daf Yomi learners study Yoma after Shekalim and not Rosh Hashana. Why is there a discrepancy between the standard Shas and Daf Yomi?
The answer has its roots in an alleged murder mystery, a curse of the saintly Rebbe Akiva Eiger, and modern copyright law journals.
To properly put things into perspective, it should be made clear that the order that Daf Yomi follows is not that foreign after all. Indeed, it is the order one follows if one studies the Mishna. Rav Sherira Gaon offered an explanation for the order. Shabbos is first because of its importance. Eiruvin is second because it deals with the laws of transporting on Shabbos. Pesachim is next because it is the first in the order of Festivals. The collection of Shekalim culminates on Rosh Chodesh Nissan so it follows Pesachim. One is not allowed to carry on Yom Kippur, so it is the most similar “festival” to Shabbos. Therefore, after discussing Pesachim, Yoma should follow because it is similar to Shabbos that we started with. Mesechta Sukkah follows Yoma because Sukkos follows Yom Kippur. Mesechta Beitza deals with the laws of Yom Tov so it follows Sukkah. Rosh Hashana, which is also a yom tov, follows Sukkah. Taanis, which discusses fasting due to lack of rain, follows Rosh Hashana because after Rosh Hashana the rainy season starts. However, Rav Sherira Gaon specifically notes that one can study Mesechtos in any order.