The complete error:
.. (adding new bone - index 6 = Head Bone 7 ("Root") exists more than once in this file, bad skeleton!

Does anyone have any clue at all as to what causes this? The issue is clear enough, but why is this an issue in the first place? A bone number exists more than once? How?

This is my object hierarchy in 3dsmax:
http://blackearth.homestead.com/files/images/3dsmax-ObjHierarchy.jpg)

I've tried doing everything i can think of to fix this, to no avail.. i even tried rebuilding the entire skeleton. If i try deleting the bone in question, it'll just error out on another. I did a search prior to posting and found someone else who had the problem, it was never solved though - and the "Root" part in their error message had a different name.. I thought that was strange. What's this name suppose to be? I don't have any objects named "Root"... although, 'SKELETON_ROOT' used to be named "Root" long ago (and that was on the olde skeleton too).... i'm totally confused.

I've been exporting with the XSI 3.0 plug-in released in the JKII SDK for all this. I can however export with the dotXSI plug-in and this error never occurs, but when i do that the mesh gets ****ed up for some reason... so i guess that isn't an option.

You're trying to compile a new skeleton with animations, right? The XSI 3.0 exporter from Raven or any XSI exporter, adds the root and effector to every bone chain, since that's how Softimage XSI and 3D handle the chains.
The problem comes because you're using the latest version of carcass, the one that compiles the XSI 3.5 files. For some reason that version goes bananas when trying to compile XSI 3.0 files that make it's own skeletons.
Use this version of carcass for what you're trying to do Carcass for XSI 3.0 (http://www.cortocg.com/base/tools/carcass30.exe). Call me in the morning.

Huh.. alright then. Yeah, i'm making a new skeleton with anims. I just noticed that it'll only error out if there're multiple bone roots.. so what you've meantioned must be the reason for that.

Is that version of Carcass the same as the one from the JKII SDK? 'Cause i did try using that and it compiled fine, to my surprise. I just thought it'd be best to use the latest one.

Also, is there an XSI 3.5 plug-in available anywhere then?

Thanks for the info.. you certainly know your ****. :D

I don't know if there's an XSI 3.5 plugin for 3dsmax. I use Softimage XSI, and export all my files as XSI 3.5, because you can choose the version :P.
However, I'm forced to use the XSI 3.5 version and the latest carcass since the first one won't compile my animations. I don't know if there's another advantage from one version to another besides the fact one compiles 3.5 and the other 3.0. Looks like all the mess comes when trying to make new animations.