Yeah, the same happened to me.I have had a sandstorm 100 percent of the time i go to the desert. I started a new game from scratch and its pretty hard to move around in there when it always happens.
The only time it seems like i haven't seen one is if i stay in the desert for like 5 mins and it eventually stops but when entering it for the first time its always there.
I decided to do a new playthrough with a char from scratch, but as I couldn't cross the desert, I had to bring wings from another character =/