Some of the things you are saying do make sense to me. Let's start from the beginning.
What system firmware are you running (sysnand)?
What emunand firmware are you running ?
--both can be found in system settings of the respective firmware
What version of the launcher,dat are you using? 3.1.1 is the latest
Old 3ds or now 3ds?
What is the exact procedure you are using to attempt to update the gateway card and causes the black screen?
I ask this becuase if the gateway card needs to be updated the gateway menu will prompt you to update it. If it doesn't you don't need to do anything. All that is required to run the latest GateWay release is to put the new Launcher.dat in the root of the internal mSD or SD card and run an appropriate exploit such as cubic Ninja, OOT, web browser or DS profile. The exploit you should be using is dependent on the model of 3Ds you have and the sysnand version.