There are two bugs in PDFGraphics2D.applyColor.
Firstly, when applying a color with CMYK colorspace the number of components is 4, not 3.
See line 744:
float cComps = c.getColorComponents(new float); //results in ArrayIndexOutOfBoundsException
Secondly, Color.getColorComponents returns values in the range [0, 1] while PDFColor expects them in the [0, 255] range.
I attached the patch and a sample program to reproduce the trouble.