Sounds like your supervisor's giving you a bonus: a lesson in vocabulary skills! Your emoluments are your earnings for the first pay period. So, she was handing over compensation — in the form of a paycheck — for all your hard work.
On the second week of my summer job at a bookstore, my boss handed me an envelope with what she called my emoluments. Looked like a paycheck to me, though.
You can find reference to emolument in many works of literature. For example, here's how author Joseph Conrad wove the word into his novel Lord Jim:
Nobody, however, had been there, and I suspect no one desired to go there in person, just as an astronomer, I should fancy, would strongly object to being transported into a distant heavenly body, where, parted from his earthly emoluments, he would be bewildered by the view of an unfamiliar heavens.
In Ulysses, James Joyce wrote:
Added to which of course would be the pecuniary emolument by no means to be sneezed at, going hand in hand with his tuition fees.
And from Nathaniel Hawthorne's The House of the Seven Gables:
They possess vast ability in grasping, and arranging, and appropriating to themselves, the big, heavy, solid unrealities, such as gold, landed estate, offices of trust and emolument, and public honors.