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When trajectorizing the 2d data, the results seem to be different depending on whether the the take's timeline has been scrubbed and the skeleton successfully mapped to the point cloud. Is it normal procedure to have to manually find a decent skelton mapping before trajectorizing?

Generally cleaning up the data first is going to give you better trajectorized data

I will generally scrub over the first few frames of animation and cut them right out to avoid excess garbage at the beginning. That seems to help the skeleton snap into place better. Then I'll clean up the data and finally trajectorize it like Vincent mentioned.

What is the advantage of cleanup before trajectorizing vs. after?

I miss quoted the info. You can only clean up the data after it has been trajectorized.

Actually you can clean up the data before being trajectorized, you just can't do it by selecting a marker in the view port only by checking the box of the marker you are editing. Here's what I've found in my tests with working between Arena and MB (Version 2010 in my case).

If you check a box in the editing panel for the marker then you can see the curves and edit them and clean them up. Then when you trajectorize the data it saves the changes you made, then you can right click on the trajectorized data and send to FBX.

If you are cleaning up the trajectorized data, then you MUST save your changes before you export to FBX. If you don't then it seems that not only do the changes not get exported to FBX but you also lose the changes you made to your trajectorized data and have to start over. (Guessing this is a bug)

If you clean up the trajectorized data and then save and then export to FBX then all seems well.

Vincent, feel free to correct me if I'm wrong in any of this.