Last I heard, moving multiple axes at once may cause issues (possibly related to Arduino power juggling).
Can you try breaking up your moves into single-axis movements? This will make your bot take a bit more time to get to places, but may increase its accuracy. If you insist on moving multiple axes, try moving X and Y together, and in a separate step move Z.
You can also try increasing the output power of the stepper drivers. Use a multimeter if you do.