Can you upload your blend file, or at least a test case which reproduces the problem?

I created a test case that perfectly reproduces the issue.
Here's the blend file to it if you want to test it:
https://www.dropbox.com/s/765rpe4ap9pbgij/ReplicateTest.blend?dl=0
Bear in mind that, in the case of the actual blender save, I'd prefer to have the 'pieces' to the main object categorized as such. They can be exported individually, but not as a group (as I'd prefer to export whole 'characters' along with the base pieces for the ease of users in the future).
I'd put the actual blend file up but I'm sure you wouldn't care for what it is.

[EDIT]
I've discovered a way to fix the issue that I'm surprised I hadn't seen beforehand.

To fix this, you just need to add the skeletons of the respective objects to the same group as the objects themselves. However, that's kind of inconvenient, and I would greatly appreciate a possible fix for that (perhaps to search for the skeleton by modifier definition and ignore parenting?)

[EDIT 2]
The same error also arises if the skeletons are in pose mod/something other than object mode.

Having multiple armatures on the same exportable is unsupported, as it allows behaviours that Source doesn't support and also opens up all sorts of complications with regard to bone names etc.

The bug was that this wasn't detected between grouped objects. Now you will receive a user-friendly warning when you try to export your scene.

To fix this, use one Armature for everything. By using bone layers and groups you should be able to achieve everything you need with one object.

You can still have whatever parenting system you want...just don't use Armatures for it. :)