I'm thinking like Mumps on this. Please try one GPU in the top blue slot, and then the second GPU in the bottom white slot. Just skipping the one slot (the lower blue one will be empty) in between the cards will make all the difference.
Manually set the fan speed to 60 or 65% in Afterburner. Drop the RAM speed on the GPUs all the way down in Afterburner, this will help cut the heat and will not cost you any credits.
The big fan on the side of the HAF-X is blowing in, the top fans are blowing up (out) the front fan is blowing in and the rear fan is blowing out -- I had one of these cases before the ThorV2 and I can say it is very nice for airflow and 2 GPUs if setup correctly.
Hope this all helps! Awesome you got the new card so soon.