Alright, sure, I'll go delete the stuff, and send you the .blend, .qc (and .vrd), and .dmx files. Then I'll post another comment.

The DMX files aren't anything special, just binary stuff that are meshes with bones and such when re-imported, but without vertex groups at all (so I won't bother uploading them).
But try reproducing the problem again, make something with DMX where you have more than 16 groups to export, then use scene export. If you can't get it to work, I can try cutting out the special stuff, and sending you the .blend session.

And? If it doesn't export the weight-map anyway, I think the chance of SMD working is small.

Note: This MIGHT only affect DMX exports, I haven't tested SMD exports like this (since DMX is a much better format in my opinion).

I have a Blender session where I took the hard-ware morph Scout from sourcesdk_content/tf/modelsrc/scout/scout_morphs_high.dmx, and over-bodygrouped him.
Then I assigned all objects into groups (most objects came into several groups, to allow me to just "Scene Export" different toggles of bodygroups), and hit "Export" > "Scene Export".
A while later, "32 files exported in 6.5 seconds" (which matches the fact there are 32 groups of objects, so it exported the right amount).
Then I compiled the model (to the FilmMaker's "usermod" folder's models and so on), and checked it in the Model Viewer.
Most things/bodygroups are rotated down into the ground and pointing away to the left[sta.sh] of the model ("$upaxis y" was used for the model, and the objects were exported with Y as up axis).
Different toggles of the bodygroups are randomly either working or down in the ground.
I checked some sequences, producing the same result[sta.sh]. (Added in a fade tint of the bones there, to show the bones are "working".)
According to the bone list, there are bones for the in-Blender/in-DMX object names[sta.sh] for the meshes that rotate derpfully, and those bones are located at 0,0,0, even though I didn't make those bones in Blender.
So I went to check the actual .dmx exports in Blender. The bones are there, but... posing them in Pose Mode does nothing to the actual mesh, and according to the "Object" tab in Blender, the meshes that don't work have no vertex groups at all, even though they work just fine in the Blender session I exported from.
A work-around seems to be exporting all files one by one, but with 32 files, and most of them not working... After counting the derped bodygroups, it seems that 16 work, and 16 don't. 16, the special hexadecimal F number (as in 0-F, not buck). Can Blender only export 16 files correctly at a time?

Using version 2.0.1 of the Source Tools in Blender 2.69 on a 64-Bit Windows 7 laptop.
And before you ask, I will not upload the .blend session, since it contains some custom things I don't want to give out. Sorry.

And the subfolder string iiiiisss... where?

Edit: Found it. Silly me, being so blind.

Yeah, basically, I find it quite unnecessary to go to the anims folder, copy an animation I exported, go back to the root folder of the anims, paste it, then delete anims, every single time I export any animation of anything. It would be nice with a checkbox or something of "Put animation files in subfolder" and then a string of what the subfolder's name should be, if the checkbox is checked.
Since I think you all understand what I mean, I won't bother explaining it 120% clearly, since I'm quite bored and tired (and drunk, if you prefer). But yeah, is there such a checkbox and string? At least checkbox? If not, I'd like to put it as a suggestion that could maybe get added in a later version or something, as I'm uncomfortable with editing the code of the plugin by myself to change the path animations export to, just to end up breaking the whole plugin.

Not submitted to Bug Reports, as this is merely a question/suggestion.

Actually I'd find that "import relative to current shape" more as a feature than bug, but sure, other people would definitely find it a bug. :P

...What can be done? As in fixed and such? Also, apparently, if you are "viewing" a shape key when importing .vta flexes, the flexes will be relative to the viewed flex, which also distorts the model in pretty much the same way as up above.

Also, what about the fact that if one imports 2 or more .vta flex files, or has made a Basis shape key before importing flexes, then there will be Basis.001, Basis.002, Basis.003, and so on, since it makes a Basis shape key for every import (even though they do nothing and are unused)?

Try closing and re-launching Blender, and then taking a screencap of the whole Blender Screen, not just the non-useful out-grayed button.