The answer to this is that Sam Gridley makes two kinds of flour -- flour from two different kinds of things.

The first thing that Sam uses to make flour is acorns.  These are the seeds of oak trees.  We find out that Sam has made this kind of flour very early in the book.  This is when we hear what Sam is doing during the snowstorm -- before we find out how he got up on the mountain in the first place.  This is page 9 in my book.

The other thing that Sam uses to make flour is the inner bark of a poplar tree.  We find this out on page 66 of the book.  Sam says it is very boring to make this stuff into flour.