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I ended up with the same problem and here my analysis:
When building using Xcode.app, we can see that source trees are set in environment variables (when variables are dumped in the logs).
setenv SOURCE_TREE_NAME=/path/to/source/
Using Jenkins plugin which calls the command line there is no such line in the logs.
Looking at the xcode-plugin code, XCodeBuilder.java does not have a source tree parameter. It should be added.
A solution could be to read the preference file ~/Library/Preferences/com.apple.dt.Xcode.plist and extract the value for the key named IDEApplicationwideBuildSettings. This is a dictionary where the keys are the source tree names and the values are the associated path.
Another solution would be to provide a new section in the xcode plugin page so that we can set source trees.
A workaround may be to set these variables with the setenv plugin, but I haven't tested this one yet.
Some interesting links: http://stackoverflow.com/questions/12010718/configure-xcode-source-trees-from-command-line
http://www.cocoabuilder.com/archive/xcode/283358-xcodebuilds-fails-where-xcode-app-succeeds-source-tree-problem.html
Hope this helps.
Olivier