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According to the standard Shas print (Vilna Bavli), the order of Masechtas is Pesachim-Shekalim-Rosh Hashana-Yoma-Sukka-Beitza. This makes (some) sense as this is the order of holidays.

However, the Bavli Daf Yomi schedule is Pesachim-Shekalim-Yoma-Sukkah-Beitza-Rosh Hashana-Taanis. I note Daf Yomi was instituted after the Vilna print.

Why is there a discrepancy in the order?

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The Daf Yomi's order is the order found in Mishna/Tosefta. In fact your real question is why the Vilna printers messed with the order. I'm guessing it had to do with size constraints on different Masechtot being in one volume. –  Double AA Oct 20 '13 at 21:23
Note also that the Vilna edition is based almost entirely on Bomberg's edition. –  Double AA Oct 20 '13 at 21:41
@DoubleAA all the more so –  Shmuel Brin Oct 20 '13 at 21:45
Or the less so. Bomberg wasn't Jewish. –  Double AA Oct 20 '13 at 21:47
@DoubleAA but it's traditional –  Shmuel Brin Oct 20 '13 at 23:24

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