This problem is due to "jp" layout's been forced by
/usr/share/ibus/component/skk.xml.
By changing to the "default" from "jp",
you can use the keyboard layout of the system default.

$ diff -u /usr/share/ibus/component/skk.xml{.orig,}
--- /usr/share/ibus/component/skk.xml.orig 2014-01-02 21:24:46.918087412 +0900
+++ /usr/share/ibus/component/skk.xml 2013-12-30 20:53:39.000000000 +0900
@@ -18,7 +18,7 @@
  <license>GPL</license>
  <author>Daiki Ueno &lt;u...@unixuser.org&gt;</author>
  <icon>/usr/share/ibus-skk/icons/ibus-skk.svg</icon>
- <layout>jp</layout>
+ <layout>default</layout>
  <longname>SKK</longname>
  <description>SKK Input Method</description>
  <rank>70</rank>

I attached the patch for ibus-skk package.

Thanks.

-- 
Regards,

Hajime MIZUNO <mizuno...@ubuntu.com>
Key fingerprint = 9B07 B934 B70C 8482 8892  E276 502E 0713 4EEF 9E8D
Description: use the keyboard layout of the system default
 Avoid mismatch with non-JP keyboard and forcing JP keyboard layout,
 by specifying layout as "default". Some of ibus-skk users use it with
 non-JP keyboard such as "US", and forcing "JP" keyboard layout annoys
 them. This patch will solve it.
 .
Author: Hajime Mizuno <mizuno...@ubuntu.com>
--- ibus-skk-1.4.1.orig/skk.xml.in.in
+++ ibus-skk-1.4.1/skk.xml.in.in
@@ -18,7 +18,7 @@
 			<license>GPL</license>
 			<author>Daiki Ueno &lt;u...@unixuser.org&gt;</author>
 			<icon>${pkgdatadir}/icons/ibus-skk.svg</icon>
-			<layout>jp</layout>
+			<layout>default</layout>
 			<longname>SKK</longname>
 			<description>SKK Input Method</description>
 			<rank>70</rank>

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