Ok , i did'nt thad the the latest Bones version , so i updated and continuing to test
Don't know if it's of any help for anybody , but i found out that maybe some export problems
are coming not from the exporters , but from the character rigs.
On creativecrash.com , i found a lot of skeletons with controls inside the bone hierarchy ,
This could be an issue when exporting animation , because the controllers would potentially not be recognised
as bones by the exporter , while being inside a bone hierarchy , and it would result in breaking bone hierarchy at export.
In ogreMax Xsi , i had several exported controllers set at origin ...
So I think it's a good idea to have the controllers outside the skeleton , controlling it using constraints.
Before export , you can use any utility to bake constraints into animation curves on the bones
( select the bones hierarchy , and go in edit/keys/bake simulation in maya , or plot animation in softimage )
and then , remove everything , but the bones and the meshes before export