I can confirm this bug. After I upgrading to Jaunty from Intrepid, Smart Pinyin 
disappeared from the SCIM menu. Also the Smart Pinyin module has disappeared 
"IM Engine"->"Global Setup". Removing (purge) and reinstalling scim-pinyin does 
not help.
However I have found a simple workaround:
cd ~; rm -r .scim
then logout and login again.

Obviously the configuration in the home directory was messed up. But I
have never tweaked the configuration files myself (other than using the
SCIM setup GUI). So I think the Jaunty upgrade process messed up SCIM,
although I have no idea why it would happen.

On the Chinese Ubuntu Forum I've also seen a report of Smart Pinyin missing in 
SCIM, after upgrade KUBUNTU to Jaunty (The link is in Chinese):
http://forum.ubuntu.org.cn/viewtopic.php?f=38&t=182934
So I am pretty sure there is something wrong with the upgrade process.

** Changed in: scim (Ubuntu)
       Status: Invalid => New

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Smart Pinyin input method is missing
https://bugs.launchpad.net/bugs/363088
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