plot.window arguments being ignored?

Hi,
Why, when I run the script below, is my y-axis range command being
ignored?  I.e., the y axis graphed consistently fits the line specified in
the plot command, but never fits the line I'm trying to add in the
subsequent line command.
This is my first R script, so if I'm doing anything else wacky that jumps
out, please let me know.  I'm an advanced Stata user, but R is new to me.
The script is designed to simulate a binary-choice decision field theory
example with internally-controlled stop time, as per Neural Networks 19
(2006) 1047-1058.
Thanks in advance!!
-Dan


#-----------------
# Starting preference state; two choices
preference<-c(0,0)
# Preference threshold; when one of the preference states exceeds this
threshhold, deliberation stops
theta<- 2
# Contrast matrix
contrast<-array(c(1, -1, -1, 1), dim=c(2,2))
# Value Matrix; three possible states of the world
value<-array(c(1,0, 0, 1, .5,.5), dim=c(2, 3))
# Feedback Matrix
feedback<-array(c(1, .5, .5, 1), dim=c(2,2))

# Time
t<- array(0, dim=c(1,1))

# Arrays to keep track of history for graphing
time_for_graph<-array(t, dim=c(1,1))
preference_for_graph<-array(preference, dim=c(1,2))

# Moving through time until preference crosses the threshold theta
while (preference[1]<theta && preference[2]<theta) {  
	
	#stochastic weights for this time period
	weight<-rnorm(3,0,1)
	
	#updating preference
	preference<-feedback%*%preference + contrast%*%value%*%weight

	#updating history
	t<-t+1
	time_for_graph<-rbind(time_for_graph, t)
	preference_for_graph<-rbind(preference_for_graph, array(preference,
dim=c(1,2)))

	#updating graph ranges
	ry<-range(preference_for_graph)
	rx<-range(time_for_graph)

	#updating graph	
	plot(time_for_graph[,1], preference_for_graph[,1], type="b",
plot.window(rx, ry), xlab="Time", ylab="Preference")
	lines(time_for_graph[,1], preference_for_graph[,2], type="b", col="red",
ylim=ry)
}
#-------------