SeaDAS' primary purpose is to display and manipulate data products produced by the OBPG.
Recognizing that users may have a desire to display custom products, several years ago we
implemented the 'Generic HDF' option. Unfortunately, it is not perfect - as you discovered.
The situation you describe, however, should have been handled within the current load routine.
There is an option to reverse the lat/lon arrays - often necessary as IDL reads the data from bottom
up, not top down...Did you check the box in the GUI (or use the img_reverse keyword on thecommand line implementation
As we are currently actively developing the next version of SeaDAS, there will be no effort
put into improving the current version's ability to navigate generic user created HDF files.
I apologize if this answer is unsatisfactory to you, but our staff and time are limited.