This question is specific to kukke Subramanya temple present in Dakshina Kannada District of Karnataka (refer : https://en.wikipedia.org/wiki/Kukke_Subramanya_Temple).
The main presiding deity is Subramanya i,e, a Shaiva deity. But the governing mutt belongs to Madhwa sampradaya i.e. Vaishnava sampradaya. Does anyone know the reason for this? Just curious to know the real history.
Also, as per temple history, Adi Shankaracharya stayed here during his digvijaya yatra and composed strotra praising the deity. So why not a Shankara mutt in this place? Just curious to know the real history. No question of hurting any faith here.