I only use Photoshop and some programs of my own.
Make sure that you're using the pencil brush for pixeling if you aren't already.
Pixels might not appear if you use pressure sensitivity and a regular brush in
indexed mode. I prefer to work in RGB 24 bit mode, then index later on.
If I have a large palette I colorpick from it, and paint like usual. You don't lose
much when indexing that way. With a large palette I might still dither, because
it's nice with some texture here and there and it helps gradient control when you
finally index.