No, it’s not the customiser, it’s the colour select box in the post section.
But, if it’s a bug with WordPress 3.9 then I guess they will fix it, but I will write to them, there are other weird things, but the inability to choose to change colour of font is a real problem.
As for my side note, regarding colour customisation, I have always found that temperamental, but it could just be me and the way I do things when I lay out a post, which up until now has not really been a problem because I could also change the font colour as I went along..
The main titles always stay the colour I want, but any other titles are a bit hit and miss, but again, I think it’s me not the theme
Maybe I will revert back to 3.8 until they sort it out..