Hello Pangloss
I have a few of questions:
When you say "Bring in mocap data", do you mean that you have the exact same character in MontionBuilder as you do in Maya, and you are just transfering the animation from one software to the other?
If this is the case, then you should not have any problems at all. When you are importing the FBX file into Maya, you only need to select the root of your character in Maya, and import the MotionBuilder character using "Update Animation" as the File Content in the FBX options menu.
If this is not the case, meaning that the skeleton in MotionBuilder is NOT the same as the skeleton in Maya, then you need to proceed differently. You have to first import the FBX file into Maya using "Add" as the File Content. Then, using the Human IK Took, you retarget your Maya character to the MotionBuilder character by setting the MB character as the Source for the Maya one.
(You should know that you cannot work with marker data, or raw mocap data in Maya. You need to process it in MotionBuilder, bake it to a skeleton, and then bring it into Maya using one of the methods mentioned above.)
Something else to consider is the Quarternion interpolation mode. This is a setting found in the options section of the Import FBX menu. Usually, using the default Resample as Euler interpolation is fine, but I am mentioning it here just so that you are aware of something else that could be checked. For more info on the Import options, you can find it in the docs here:
http://download.autodesk.com/us/fbx/2012/maya/index.htmlIf your skeletons are not the same, and you are not using the HIK Tool to retarget, how are you retargetting your animation?
To answer your question about rotations on MotionBuilder, there isn't a method to "Zero Out" the values as in Maya. But, the plug-in designed to compensate for this fact. I have run tests with skeletons that have Pre and Post rotations in MotionBuilder and they transfer correctly into Maya.
Finally, if you like, you can send me your character and your animation file. That way, I can see if I can duplicate your problem here and find a solution for you. If you don't want to post your files online, you can send them directly to me through email. carlos.carpintero@autodesk.com Whatever we receive is considered confidential and private, not the be shared. (Please include the version of the FBX plug-in you are using)
As usual, if you have anymore questions, let us know.
Regards,
Carlos