I just found out how to fix this - on my Kyocera Mita FS-C5400DN the Cyan and Magenta colors were greatly misaligned. Cyan was 3 mm to the left and magenta was about 9 mm to the left (misaligned).
In the "Advanced Operation Guide" I found out that I have to go to Menu-> Adjust/Maintenance -> Registration Normal. Use "Print Registration Chart" and see which colors are misaligned.
The center lines on both black and color bars should perfectly match. If they do not, go in the same menu and select "Adjust Magenta" or Adjust Cyan/Yellow depending on which color is misaligned.
Look at the printed chart and select the best matching line. If it is greatly misaligned then select the farmost value. E.g. if the magenta bar is greatly to the left - select "I", if to the right - select "9".
Please note that the alignment values are added/subtracted and stored each time you change them and press OK. The values increment or decrement the alignment each time.
Also take into account that for farmost values the left and right portions both will vary slightly even if you adjusted just one of them.
I hope this helps anyone looking for the answer!