From my experience there are 2 mains things might not be set up
1) You must have the JDK version of java. The SE version lacks some tools that the code will try to use.
2) Make sure the JAVA_HOME is set in your path. I don't think anything will have set this unless YOU have set this manually yourself.
Go to the command prompt and enter this:
Look at the text returned and make sure you see jdk1.7.0_55 or something similar in the big long text. Must be JDK.
2. Again at the command prompt type
Again make sure this mentions the jdk path.
Mine says JAVA_HOME=C:\Program Files\Java\jdk1.7.0_55
I think I had to set this manually. If you don't know how to do this google 'Set java_home windows' and you should find something.
If you're still getting a problem you could try deleting the <XXX>.Aligned.apk file in the APKs directory as I think my exe didn't force an overwrite if the old one was in there (though I'm not 100% sure it was needed).
If you are struggling post the results of 'SET PATH' and 'SET JAVA_HOME' back in this thread.
I thought of something else that caught me out. Make sure the alias for your keystore is correct. I think I had created mine on the GC website wtih a default of 'mykeystore' (https://developer.thegamecreators.com/android/create_keyhash.php) but I think the APK Builder was defaulting to 'My Keystore'.
I would also say that if you're struggling a bit the web version seems to work fine and there is less to trip up over using that if you need to get started quickly:
http://developer.thegamecreators.com/android/create_apk.php
Cheers,
Michael