The student took a leave of absence for a year and received a new I-20 and paid the SEVIS fee again.
The visa was valid, but the SEVIS ID on the F-1 visa was different from the newly issued I-20. The Immigration Officers put the student into the secondary inspection which caused a longer immigration time but the student ended up entering the U.S. successfully.
The takeaway is that students could be placed into the secondary inspection by CBP (immigration) officers but per regulations, students can be confident that they can enter the U.S. with a valid visa even though the SEVIS ID appears on the visa is different from the one in the I-20.