You are correct that the joints orient the wrong way on the left due to mirroring. Someone (over a year ago now, wow) once told me that they had difficulty getting mirroring to work in a maya to ee pipeline (this topic here:
http://www.esenthel.com/community/showth...tid=4018).
I have looked at your original maya file, and I would have to say that mirroring is definitely a problem there. You can try the following:
1. in the file, press F8 to go to component mode.
2. In the selection mask toolbar (it replaces the one that lets you toggle selectable meshes, joints, etc), click on "select miscellaneous components" -- it looks like a question mark.
3. select the right Lower leg Joint, zoom in to where the knee is)
4. Select the XYZ locator axes. When you do so, it will highlight.
5. Press E to go to rotation.
6. Rotate the joint just a bit. And then Undo your change (i'll show why in a second).
7. Open up your script editor. You can find this in Window -> General Editors. (Forgive me if you know this already).
8. In your script editor, find the line "rotate -r -p -9.87426cm 50.0987cm -5.20124cm -os -21.392798 0 0;"
* -- your line may be slightly different. The important thing here is that you understand the 3 numbers after the -os "-21.392798 0 0;" This is the X Y Z coordinates of how we are going to rotate our pivot and is the portion that we will be editing so we can make a command to rotate those pivots for you further below.
9. Copy the whole line of the command and paste it in your script editor input window (the lower half of the script editor).
10. Edit the line so that the last three numbers after -os says: -180 0 0;
My line, for instance now says: rotate -r -p -9.87426cm 50.0987cm -5.20124cm -os -180 0 0 ;
11. The pivot should still be selected in your panel. With it selected, hit the play button in your script editor. You should see the pivot's Y and Z change orientation, while the X still points down the joint chain.
12. Repeat this for each of the joints that were mirrored that has this problem, then export and test to see if it's made a difference in EE.
Ineffable: Sadly, I do not know much about Blender. I am sad that you are experiencing the same issue but relieved (slightly) to see that the experience is not limited solely to maya.
I imagine that Blender offers a way to adjust the pivots on your joints. If the situation is similar to the one that we have in Maya, you will want to make sure that the X-axis of the joint points down the chain to its child. In areas where the chain would split (for example, where the back bone branches off to make right and left arms) - you want to make sure that the back bone is oriented to follow the neck, and not one of the arms. Another trouble spot for me was where the hand branches off to each of the fingers - i ended up aligning the hand joint to follow the middle finger.