Jews living in the Diaspora (outside of modern Israel) typically observe two days of chag on holidays that are Yom Tov (holidays where work is forbidden, called yontiff in Yiddish). In Israel, only one day of chag is observed.
Sometimes, depending on the calendar, the Diaspora observes the second day of chag on Shabbat, and the holiday Torah reading pushes the regular weekly Torah reading back a week. Since Israel has only one day of chag, they read the regular weekly Torah reading. Thus, the Parashat ha-Shavuah ends up being different.
When using the “Weekly Torah portion on Saturdays” option on the custom calendar, select the appropriate option depending on where you live (Israeli holiday schedule for those living inside Israel, Diaspora for everyone else).