Run the obfuscator in verbose mode

It might happen that the obfuscation does not work as expected. In this case there may be some "strange" folders in your project and the generated plugin jar contains non-obfuscated classes.

But the build process runs in headless mode and no errors or warnings are printed out in the console view.

The easiest way to debug the obfuscation process is to create and execute a build.xml file for the plugin.

At first generate a build.xml file by clicking on PDE Tools > Create Ant Build File in the context menu of the project or the META-INF/MANIFEST.MF file.
Then run the build.xml file by clicking the Run As > Ant Build entry of the context menu of the build.xml file.
The output of the plugin build is shown in the console view. Warnings and error messages are highlighted.

The target post.@dot contains the messages relevant to the obfuscation. In the above screenshot there is a error message:

[subant] Failure for target 'post.@dot' of:
          /prj/de.partmaster.mytest/customBuildCallbacks.xml
[subant] The following error occurred while executing this line:
[subant] /prj/de.partmaster.mytest/customBuildCallbacks.xml:119:
          Problem: failed to create task or type proguard
[subant] Cause: The name is undefined.
[subant] Action: Check the spelling.
[subant] Action: Check that any custom tasks/types have been declared.
[subant] Action: Check that any <presetdef>/<macrodef> 
            declarations have taken place.

In this case Ant could not find the declaration of the proguard task. This should not happen in practice – otherwise check your Eclipse installation in Help > Software Updates > Manage configuration for broken plugin dependencies.
As a rule of thumb you should follow make sure that you

1. rebuild the customBuildCallbacks.xml file if you change the package structure of the plugin,
2. rebuild the build.xml file if you change anything in customBuildCallbacks.xml.
3. run the build.xml script in verbose mode if you cant find the error.
4. Attach the verbose console output together with the file proguard.properties to any bug report and name the version of Java and Eclipse you are using.