As Randy pointed out above, some media is designed for screening or cutting, some is designed for actual printing. In the case of the Mutoh, my understanding is the heaters actually open up "pores" on the media (yes, vinyl does have these pores) which allow the inks to be impregnated into the material, thus giving the image longer life and UV resistance. The solvent components act as carriers for the pigment and then the post-heater bonds the ink to the material.
It could just be the 3M prrismatic is not manufactured to a digital printing spec, thus the varying degrees of success with the product. Being that you have had some success, have you tried playing with your saturation levels a little bit or perhaps a different profile to see if it makes a difference?