Motionbuilder 2018 SDK breaking changes

So I have a plug-in that is using setMatrix to stream anim data to a skeleton in mobu from an external device. It was working just fine in 2016, but in 2017 and up the local trans and rot values go completely haywire. It looks like joints got remapped, but nothing has changed in the heirachy or the anim data. Anyone know of any changes to the SDK or the FBmodel class that would cause this?