Welcome to the forums! Just a couple of questions:
What firmware version are you referring to that's only for the EM-406? Are you referring to the same firmware version (F-GPS-03-1203062)?
And, what firmware version that you flash to the EM-406? Where did you acquire it from? Please keep in mind that upgrading the firmware of the unit without proper instructions, you may render your device unusable.
Also, in order to provide further support, can you please register your product and generate a support ticket? Please check your email for further instructions.