Changing proguard.bat as suggested didn't help in my case. Upgrading to proguard 4.6 also didn't help. What helped me is that I had to downgrade to Android SDK tools to revision 11.
Note: when running SDK Manager and installing packages, I didn't install package "Android SDK Tools, revision 12".
UPDATE:
I have tried with Android SDK revision 15, but the issue is still present. Now this workaround of downgrading to revision 11 does not work any more, as URL that SDK Manager is using to download packages is not working any more.
After 2 days of trying different solutions, upgrading to proguard 4.6 did help.