It usually means that one of your bone has a scale on it. Please check if it's the case.

Here is the mel script to make sure no scale is applied on any bone:

string $joints[] = `ls -type "joint" -long`;
print $joints[0]; //the first joint
* loop through all objects */
string $joint;
for ( $joint in $joints ) {
setAttr ($joint + ".scaleX") 1;
setAttr ($joint + ".scaleY") 1;
setAttr ($joint + ".scaleZ") 1;

To be able to create Apex files, you will need to install the Nvidia Physics DCC plugin from Physics SDK 3.4 (or older version)

(as of 2017, July 10th) You need to create an account on Nvidia developer zone https://developer.nvidia.com/

Then visit this URL to find the package directly: https://developer.nvidia.com/gameworksdownload#?tx=$physx_sdk,3.4.0

Note that Nvidia does not provide a package for Linux, so unfortunately, you will not be able to create Apex files from a Linux workstation