Still an issue over five years later. I just spent a little time writing an expression, because the order that the default "dimension" filter colours things is not consistent, annoying the users. Only the expression gives me the power to control this, but then I lose the key, so nobody would know what the colours even mean (unless they hover the mouse over the stack on the bar).
The expressions aren't great either, because I then have to write one for every single stack, when I only want to customize a couple of them.
All in all, colours in Qlik are pretty rubbish, poorly designed and a real headache.
