Is it possible that the original poster had the Hmisc package loaded?

Hmisc::reorder.factor
function (x, v, FUN = mean, ...) ordered(x, levels(x)[order(tapply(v, x, FUN, ...))])
<environment: namespace:Hmisc>

Without that package, reorder.default gets called:
getAnywhere('reorder.default')
A single object matching ‘reorder.default’ was found
It was found in the following places
  registered S3 method for reorder from namespace stats
  namespace:stats
with value

function (x, X, FUN = mean, ..., order = is.ordered(x)) {
    scores <- tapply(X, x, FUN, ...)
    ans <- (if (order)
        ordered
    else factor)(x, levels = names(sort(scores)))
    attr(ans, "scores") <- scores
    ans
}
<environment: namespace:stats>

                                        - Phil Spector
                                         Statistical Computing Facility
                                         Department of Statistics
                                         UC Berkeley
                                         spec...@stat.berkeley.edu



On Tue, 5 Oct 2010, Joshua Wiley wrote:

sessionInfo()
R version 2.11.1 (2010-05-31)
i486-pc-linux-gnu

x <- factor(1:5)
x.ro <- reorder(x, rnorm(5))
is.ordered(x.ro)
[1] FALSE
x.ro <- reorder(x, rnorm(5), ordered=FALSE)
is.ordered(x.ro)
[1] FALSE


On Tue, Oct 5, 2010 at 3:14 PM, Darin A. England <engl...@cs.umn.edu> wrote:

Or at least is seems that way to me. It's not a big problem, but the
behavior doesn't match the documentation. (I think r-help is the
place to report this. )

> x <- factor(1:5)
> x.ro <- reorder(x, rnorm(5))
> is.ordered(x.ro)  # should be FALSE according to ?reorder
[1] TRUE
>
> x.ro <- reorder(x, rnorm(5), ordered=FALSE)
> is.ordered(x.ro)  # should be FALSE
[1] TRUE


Here is my session info:
> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] splines   datasets  utils     stats     graphics  grDevices
methods
[8] base

other attached packages:
[1] Design_2.3-0    Hmisc_3.8-3     survival_2.35-8 RODBC_1.3-2
[5] MASS_7.3-7      lattice_0.19-11

loaded via a namespace (and not attached):
[1] cluster_1.13.1 grid_2.11.1    tools_2.11.1

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and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

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