Uploading textures on a mesh object with Alpha Blending/Masking

Hello. I seem to do be able to uploaded mesh objects, most with simple textures are working when then come into world.  The ones I am having trouble with contain alpha blending/masking.  When the textures are applied they are all crazy on the item and disfigured.  Is there a  box I should be checking on the import screen or am I missing a step somewhere?  If this has been asked before, maybe a link to the post would help me.  Thanks so much!