Twisting Words!

Pyth, 19 15

VPc+z*dQQ_W~!ZN

Pre-pads the string, then reverses each other line as it prints it. The padding is equal to the size of the box, but the last line after chopping up the input is discarded.

Try it here

CJam, 19 bytes

q~1$S*+/W<{(N@Wf%}h

Input example:

5 "Hello, World!"

Explanations

q~         e# Input n and the string.
1$S*+      e# Append n spaces to the string.
/W<        e# Split by each n characters, and remove the last chunk.
{          e# While the array of chunks isn't empty:
    (N     e# Extract the first chunk and push a newline.
    @Wf%   e# Reverse every chunk left in the array.
}h

Python 2, 60

s,n=input()
d=1
while s:print(s+n*' ')[:n][::d];s=s[n:];d=-d

Takes n characters at a time from the from of s, printing them with a direction d that alternates between 1 and -1. For spacing on the last line, s is padded with n spaces at the end before it is chopped, which only affects it when it has fewer than n characters remaining.

A recursive solution would save a char (59) except that it leaves a trailing newline, which is not allowed.

f=lambda s,n,d=1:s and(s+n*' ')[:n][::d]+"\n"+f(s[n:],n,-d)