In affinityinput.txt, set Test Mode to 0:
Code:
#
# WinAFC Input File
#
# Lines that start with a '#' and empty lines are ignored.
# Configuration lines include global flag setting lines, and application profile
# lines. These lines can be interleaved in any order. However, the order in which
# you specify the various application profiles matters if a process could be
# matched by multiple application profiles.
# To run AffinityChanger in TestMode (no affinity settings are modified),
# uncomment the line below and specify a value different than zero. To disable
# test mode, set the value to 0 or comment the line below.
# It is recommended that you try the input file in test mode first, after you
# make changes, especially if you are unfamiliar with the syntax.
TestMode = 0
Forgot about that part in my original post.

Sorry about that, guys and girls.
Just added it now.