Since Java 7 update 45, the Manifest has a "security" attribute that is called Application-Name
. If this attribute is not set, the main class is the name. The main class of every javafx application that is deployed is com.javafx.main.Main. So that explains that.
Read: http://www.oracle.com/technetwork/java/javase/7u45-relnotes-2016950.html
Obvious solution: add manifest attribute Application-Name
to your build process.