your slicer is screwing up your support- it's offset and apparently not by the correct offset for your support nozzle. Slic3r does not offer a lot of control of infill density IIRC.

it's going to be tough to print that design. I would change the support to be a second pla part that fills the horizontal slot but also goes inside the gasket and extends down to the bed. I don't know how well pla or abs will stick on top of ninjaflex having never used ninjaflex before.