txn_two_phase_commit_write_concern.js commits a transaction via coordinateCommitTransaction, which performs an update to the config.transaction_coordinators doc for the transaction and waits for it to satisfy the given write concern before returning. The test then validates that the write concern was respected by checking the config.transaction_coordinators doc on the expected number of nodes reflects the update.

As of PM-3489 it is no longer a valid assumption that a majority committed write has been applied on a majority of nodes yet, only that a majority have acknowledged it / made it durable. And so this test sporadically fails when testing majority WC behavior because sometimes the update has not been applied yet on a secondary.