To seal leaks properly on flutes, a procedure is used which is called "partial shimming". This involves the use of little pieces of paper of different thicknesses (shims), placed under the pad where there is a depression in the pad or tone hole. These pieces, generally 1/16" to 1/2" in size vary in thickness from .001" to .006" approximately. A tiny piece, like a pie slice, is placed or glued on the back of a pad or whole round shim, and when done properly will help to close the gap between pad and tone hole.
These gaps are caused by a not so flat pad, or a not so level tone hole. 

If partial shimming is not done,  the flute is more prone to leak, unless softer, more cushiony pads are used. The soft pads will fill up the leaking areas if it is seated by clamping, but will result in a mushier feel of the instrument, and the leaks will return when the seat disappears over time.
(Soft pads are used on all student flutes, and most commercial flutes under $2000.) 

Setting up any flute with harder pads improves the response,
and helps it stay in adjustment longer, even indefinitely.

Air can also leak through the screws and grommets that hold the pads on. 
I take great pains in sealing these leaks as well.

It can take a whole day or two to repad a flute in this manner.
Longer to set up a flute for the Straubinger pad.