HELP - Grain filler problem

HELP HELP HELP ...I ran into a dilemma with my pore filler wherein the filler in the pores is still light grey colored, even after 2 clear vinyl coats & 3 clear lacquer coats, & drying 1 day before each coat. I colored my pore filler with minwax oil-based dark brown stain before applying it. I'm using the Cardinal mahogany oil based pore filler. I also let the filler dry a week before applying a 2nd coat of filler, then dried it for another week, then sanded it down & air blew it & lightly wiped it with naphtha. Before I started the vinyl seal I sprayed it with naphtha & all the pores we're a nice dark brown, but after the naphtha flashed off a second later, the pores turned light gray again. I'll attach a pic later.