This bug can be reproduced using R version 2.4.1 for Windows, where 
WinAnsiEncoding is used.
To reproduce this bug, start a Windows R session, and run:

postscript("first.eps", width=6, height=6, horizontal=FALSE, 
onefile=FALSE, paper="special")
plot(1:5)
dev.off()
q("no")

Now, start a new R session, and run:

pdf("second.pdf")
plot(1:5)
dev.off()
postscript("third.eps", width=6, height=6, horizontal=FALSE, 
onefile=FALSE, paper="special")
plot(1:5)
dev.off()
q("no")

The differences between "first.eps" and "third.eps" are shown to be:

$ diff first.eps third.eps
40d39
< /WinAnsiEncoding [
73d71
< ]

The file "third.eps" is an invalid format, and Vhostview reports:
Error: /undefined in WinAnsiEncoding
Operand stack:
   .notdef   .notdef   .notdef
... etc ...

I've also tested for this peculiar behavior with R 2.4.1 for Debian, 
however it checked clean.
+mt

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