Got the same issue when importing photo's made with an iPhone. I used 2 tricks to get the orientation right. If there are a few photo's I open them in Preview and save them again. The orientation is then respected by FileMaker.
With a batch import (or on the fly) I use the free 360Works Scriptmaster to rotate the image 90 degree. You could also use the (not free) CNS Image plugin.
Hope that helps,
Ruben van den Boogaard