I've never seen that. Are you sure you are using the correct file for your controller and not the one for the 600-series controllers?
ArubaOS_MMC_6.3.1.6_43301
vs
ArubaOS_6xx_6.3.1.6_43301
I've gone from 6.1.3.10 to 6.3.1.6 without any problems, so I don't think there should be any issues with getting there from 6.1.3.6.