Well, i have no answer, but i believe i can give you some hints.
As i said in comment, i guess that your eps graphics files do have that "/Rotate 90" commands inside, and it's quite ok. You can check this using this command:
grep "Rotate 90" graphics.eps
(just replace "graphics.eps" with your image file name)
So, i think that the problem is with XeLaTeX's graphics driver. I can not check this, i have no such images around me.
Anyway, i would try to "re-eps" such images with eps2eps; it claims it "performs the equivalent optimization for Encapsulated PostScript (EPS) files".
Not sure that this can help, though.
Update
I've edited your EPS file (using vim), please see the difference:
%%+ font Helvetica-Oblique
%%+ font Helvetica-BoldOblique
%%+ font Symbol
-%%DocumentMedia: letter 612 792 0 () ()
+%%DocumentMedia: letter 792 612 0 () ()
%%Title: R Graphics Output
%%Creator: R Software
%%Pages: (atend)
@@ -12,7 +12,7 @@
%%BoundingBox: 54 144 558 648
%%EndComments
%%BeginProlog
-/bp { gs 612.00 0 translate 90 rotate gs } def
+/bp { gs 0 0 translate 0 rotate gs } def
% begin .ps.prolog
/gs { gsave } def
/gr { grestore } def
Here is the result -- achieved with LaTeX, not XeLaTeX (!!):

So, this is not a solution really, but rather a demonstration (i could find "better" numbers, possibly). So, i do believe that [xe]latex can not display you eps graphic files. Yes, i've tried with eps2eps with no success. Oh, well, i've replaced \usepackage{Sweave} with \usepackage{graphicx}, i hope it didn't any difference.
With XeLaTeX result is just the same with my texlive (2009-7, current Ubuntu's one, i believe).
Well, this is very attractive .)
Update 2
inkscape --export-eps=hist50-good.eps hist50.eps
This produces "good" EPS (4678 source expanded to file 78626 bytes long! but quite usable, i'd say).
inkscape --export-text-to-path --export-eps=hist50-good.eps hist50.eps
This reduses size to 40435 bytes.
As a result, correct page produced.
I think you can process all EPS files in a batch (be sure to make a backup,)
I am still not sure that this can be a solution for you.
ps. i feel like it's a bug?.. Your images are quite good, at least gv (3.6.8 here) and inkscape (0.47 r22583 here) shows them right.
vim, let's say). The problem is with xelatex's driver, i guess. Sorry, i can't help you here. – brownian Feb 02 '11 at 11:05