I have three different modules I'm tagging manually in Jenkins using version 1.439.
I'm running with the 1.37 version of the Jenkins Subversion Plug-in.
After the build completes I use the "Tag this build" link on the left when viewing the build status.
The three different modules live in two different SVN repositories and in turn have three different revision numbers.
After clicking on the "Tag this build" link the Build panel displays and the Module URL and Tag URL fields are populated accordingly.
Example:
Build #28
Module URL
http://xxx:8080/svn/hc-build/trunk/backend/hc-build (rev.207)
http://xxx:8080/svn/hc-framework/trunk/backend/hc-framework (rev.44)
http://xxx:8080/svn/hc-framework/trunk/backend/hc-framework-test (rev.36)

Tag URL
http://xxx:8080/svn/hc-build/tags/HC-Framework-RC-28
http://xxx:8080/svn/hc-framework/tags/HC-Framework-RC-28
http://xxx:8080/svn/hc-framework/tags/HC-Framework-RC-28

Commit comment:
Tagged from HC-Framework-RC #28

End-Example

So all this looks good. The URL's are correct, the revision numbers, the Tag URL's all look correct.
However when the tag is actually created the directory structure is not what I would think should be created, the top node/directory is getting dropped in some scenarios.
After executing the tag under the hc-build/tags folder I would expect to find a /HC-Framework-RC-28/hc-build folder, but instead I find the files and sub-folders located underneath that folder. Like the .classpath and .project files for Eclipse and the src folder. That top level hc-build folder is missing underneath the tag folder.
Under the hc-framework/tags folder I do have the HC-Framework-28/hc-framework-test folder and all its contents as expected, however, when it comes to the hc-framework folder, once again like the hc-build folder, I get the contents of that folder instead of the base folder hc-framework. There is no HC-Framework-28/hc-framework folder.

It looks like the tag is flattening or dropping that top level node when there is only one folder/module in the target or for multiple modules it is dropping/flattening the first module. Upon further testing sometimes it drops/flattens the last module instead of the first module. Either way one of them is getting dropped/flattened.

Any idea's as to why this is happening? Hopefully someone can recreate this.