You're now talking about accuracy; that's a whole other ball game.
I don't know if you can make it to the next
TOPAS user meeting, but Ian Madsen and Nikki Scarlett are on the speaker list, talking about microabsoprtion and data collection strategies for QPA.
You might be running into issues around microabsorption. What are the LACs of your various phases? You could be having issues of contrast between the various phases. There is no real fix for this, apart from trying different x-ray energies to minimise contrast, or to use neutrons.
You mention grinding; How are you grinding? By hand? With a microniser? Are your intensities repeatable? Try running a specimen, then tip out the powder from the holder, give it a light grind by hand to break up any agglomerates, reload the same powder, and run it again. If you do this, and your intensities aren't repeatable, you probably have a particle statistics issue, and need to grind better, or otherwise get more particles in the beam.
Matthew