There are a few ways to end up with double-quoted paths inside of double quotes, including the case where user path does not already contain any paths.
Run Engine/Extras/Android/SetupAndroid.bat without any paths in user path. This would result in trying to add """;c:\user\...." which isn't legal.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-99691 in the post.