A guess: doubly ionized helium vs. singly ionized helium. They absorb different amounts of radiation (have different opacity). At high opacity it gathers heat and subsequently expands. At low opacity it lets the heat pass through, subsequently cools and condenses.

(This is the mechanism that makes Cepheid stars regularly and predictably change intensity. The same mechanism is probably present in other stars too, and causes local processes that we cannot observe from another star system… but can observe in the Sun.)

Alternatively, there could be a multitude of other effects doing something similar.