i'm doing some dual material prints (tpu on the bottom and pla on top)
and i ran into this issue as well.
what i did to solve it (in S3d) was to make sure both extruders where in each profile, and set the the one not printing to 0 degree's
this is of course only applicable if you are printing like i am, 1 complete model on the bottom and then the next one right on tip of it with another material, that is, i'm not doing any mixing, i'm making some coasters, tpu on the bottom and pla on top works great.. now if you are intermingling your prints so there are 2 colors/materials throughout the piece, an ooze shield combined with some proper retraction is probably the best bet.