We use the stock Epson Matte Black only for the films; pigment based so we had to get film that matched. We've had one clog from lack of use, but one head cleaning fixed it and we were back to using it. The ink does not "look" as dense as the dye based film from our old 3800, but cause no trouble in exposing them. As one of the old guys, I'll reference Rubylith and Amberlith, which were transparent, yet exposed just fine...
Steve
We haven't tried 3rd party inks because we're too chicken to void the warranty, cluck, cluck, cluck...