I have similar problems with my Epson... It seems it's only in certain dark colors. Dark purples and blues seem to get it the most. When it happens to a certain file, first I try to resave the file in different formats to see if that helps ( eps, PDF, jpeg and tiff) I also try different media from oracal 3640, 13 oz banner, solvent photo paper to 3m control tac. And when it happens it happens to all the media. The funny thing in some areas it prints fine, and some of the dark areas it print with a wave pattern. I tried different heat settings, cleaning the crap out of the machine, not using the take up wheel, humidifier and dehumidifier, distance adjust (oh by the way when this first happened I called Epson tech support and they told me what does distance adjust mean... Get support guys) even tried uni-directional at a higher wave length and lower wave length ... Nothing works. Its been almost a year and after calling and calling tech support with epson (know they tell me my support has run out, never fixing the ongoing issue)
Now when I get that certain color you know what I do? Print that son of a ***** on my value jet... That's what I do!!!!