Problem with cell numbers when using a raster extent object

Hi -

I have a script that calculates a common extent between two images than then
uses the resulting extent to restrict the random selection of cells from a
raster using the ?sampleRandom? function. I use the following function:

sampleCells <- sampleRandom(predImage, size=numSamps, cells=TRUE,
extent=commonExt)[,1]

Next I use "xyFromCell(predImage, sampleCells[i])" to calculate the
coordinates of the center of a cell and all of the cell centers fall outside
of the extent that I am using. Using "sp=TRUE" I get a similar result - all
of the points are outside of the extent:

sampleCells <- sampleRandom(predImage, size=numSamps, sp=TRUE,
ext=commonExt)

To get around this problem I tried to physically clip the image before
running ?sampleRandom? and the results are similar. The following line also
produces cells that are outside of the extent ?commonExt? when I use
?xyFromCell?:

sampleCells <- sampleRandom(crop(predImage,commonExt), size=numSamps,
ext=commonExt, na.rm=TRUE)

However, if I run the following line using"clip" and "sp=TRUE" the sample
points fall within the extent:

sampleCells <- sampleRandom(crop(predImage,commonExt), size=numSamps,
sp=TRUE, ext=commonExt, na.rm=TRUE)

So, there is a work-around but I'd prefer not to have the overhead of
clipping the image.

This seems somewhat similar to a problem I reported a few months ago and was
fixed. Can anyone replicate this problem? Am I doing something wrong?

I am using R version: 3.0.2 and Raster package version: 2.1-49 on Ubuntu
12.04 64 bit

Ned