patching oddity

[Patrick Welche <prlw1%cam.ac.uk@localhost>]

I have WRKOBJDIR=/usr/obj/pkgsrc in my /etc/mk.conf, and made a patch as
usual:

quantz# pwd
/usr/obj/pkgsrc/math/glucat/work.x86_64/glucat-0.7.1
quantz# pkgvi configure
pkgvi: File was modified. For a diff, type:
pkgdiff "configure"
quantz# pkgdiff "configure" > /usr/pkgsrc/math/glucat/patches/patch-configure

then later

===> Patching for glucat-0.7.1
=> Applying pkgsrc patches for glucat-0.7.1
=> Verifying /usr/pkgsrc/math/glucat/patches/patch-configure
=> Applying pkgsrc patch /usr/pkgsrc/math/glucat/patches/patch-configure
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD$
|
|--- configure.orig     2012-11-07 11:36:36.000000000 +0000
|+++ configure
--------------------------
File to patch: configure
No file found--skip this patch? [n] n
patch: **** can't find configure
Patch /usr/pkgsrc/math/glucat/patches/patch-configure failed


Yet

quantz# cd /usr/obj/pkgsrc/math/glucat/work.x86_64/glucat-0.7.1
quantz# ls -l configure
-rwxr-xr-x  1 root  wheel  269120 Nov  7  2012 configure


The only odd thing I noticed is when unpacking the tar file, I get many:

tar: File extended headers posix ustar archive. Extracting as plain files. 
Following files might be in the wrong directory or have wrong attributes.

What happened?

Cheers,

Patrick