1 should be fine, but you say that doesn't work... Did you remember to re-export?

I know a flex controller can have multiple shapes applied, either depending on where the flex slider is, or depending on a mix of that and a "value" slider, I'm just talking about having several flexes with the exact same name across several bodygroup options. Even though you don't know how to do that, either, it was still worth a shot to ask.

By now, you should have no idea what I'm talking about.

But as an example, I'd like to bodygroup something with several different options, all of which should have flexes. That would be done like this:

$BodyGroup Lash {
Studio "Base/MareNoLash.dmx"
Studio "Base/MareLash.dmx"
Studio "Base/MareTopLash.dmx"
Studio "Base/MareBottomLash.dmx"
}

However, if I include the flex definitions text file in all of those, all flexes will be duplicated 3 times (so there are four flex sliders with the same name per flex in the model), and only the last "list" of flexes will affect the model.

But if I only include the flex definitions text file in one of the exports (that being the first one in the bodygroup list), and use a "blank" flex text file for the other bodygroup options... While there won't be duplications of every flex slider, only the bodygroup that has flex definitions will be affected by the flex sliders.
(Yes, the shape key names in Blender are identical across the bodygroups.)

By now, you should know exactly what I'm talking about.
So does anyone here know of a way to make there only be one set of flex sliders, yet have the flex sliders affect all bodygroups?

I highly doubt this is classified a bug at all by Artfunkel, in fact rather a feature. Besides, clicking that folder icon, going to the latest "Recent" folder, and clicking Accept/OK/whatever really shouldn't be that hard to do, and if one would use Blender to do something where it'd be worth it to export it, one would probably do that thing anyway.

Why wouldn't you be? After all, the Blender Source Tools allow exporting meshes and animations.

Oh. That could help, too.

I'm not sure, but it might be related to something along the lines of quad-to-tris-ing.
If you really need it as SMD, you can go into edit mode, and press Ctrl+T.
I know nothing about the bug itself, though.

Maybe because, as it clearly says itself, it can't find the ValveBiped.Bip01_Head1 bone to attach at least one of the eyes to?

A screenshot would be helpful.

I don't think ".blend" is an image extension, so I'll just not download that.