When I am working on my research, or on MO/math.SE questions, I often find myself thinking in a way which reminds me of the feel of solving Olympiad problems. If I then solve the problem, I try to find a very special case of my problem which is still challenging, and can be stated and solved using only material on the Olympiad curriculum. I then e-mail Kiran Kedlaya and say "Hey Kiran, do you think this would be a good Olympiad problem?" If he thinks so, he proposes it to the USAMO committe.
I wrote Problem 2 on the 2010 USAMO in this way; it is Theorem 3.2 of this paper specialized to the case that $W_0$ is the group $S_n$. The fact that the "total number of moves" referred to in the theorem is at most $\binom{n}{3}$ is computed in Section 5.2.
I send Kiran about 1-2 problems a year; I don't think any of the others have appeared yet.
UPDATE Problem B4 of the 2014 Putnam was mine. Let $F(x,y,z) = \sum F_{ijk} x^i y^j z^k$ be a homogenous polynomial of degree $n$ with positive real coefficients. We say that $F$ is hyperbolic with respect to the positive orthant if, for all $(u_1,v_1,w_1)$ and $(u_2,v_2,w_2) \in \mathbb{R}_{> 0}^3$, the polynomial $f(t) = F(tu_1+u_2,tv_1+v_2,tw_1+w_2)$ has $n$ negative real roots.
This paper show that there are constants $V_1$ and $V_2$ (dependent on $n$) so that,
(1) if $F$ is hyperbolic with respect to the positive orthant, then $F_{i(j+1)(k+1)} F_{(i+1)j(k+1)} > V_1 F_{i(j+1)(k+1)} F_{(i+2)jk}$ and the same for all permutations of the indices
(2) if $F_{i(j+1)(k+1)} F_{(i+1)j(k+1)} > V_2 F_{i(j+1)(k+1)} F_{(i+2)jk}$ and the same for all permutations of the indices, then $F$ is hyperbolic with respect to the positive orthant.
The proof is nonconstructive; I also (Theorem 20) give an explicit value of $V_1$. I was thinking about whether I could give a concrete value for $V_2$. The problem was too hard, so I thought instead about homogenous polynomials in two variables, which is the same as inhomogenous polynomials in one variable. At this point, I was basically looking for a converse to Newton's inequality: I wanted a constant $C$ so that, if $a_k^2 > C a_{k-1} a_{k+1}$, then all the roots of $\sum_{k=0}^n a_k z^k$ are real. The result in one variable wasn't worth publishing, but I figured I could make a nice problem by choosing a particular polynomial and asking people to prove the roots were real.