"Rule for unknown flex" means you have not made the flex lines in the QC properly.

I see what the problem is for the first animation you want to look at, "taunt_rps_paper_lose". For some reason Crowbar (0.34) does not put any data into the "taunt_rps_paper_lose.smd" file. However, searching for "taunt_rps_paper_lose" in the QC file shows the following $sequence blocks:

The "taunt_rps_paper_lose" sequence uses a layer, "layer_taunt_rps_paper_lose". Loading the scout model then the "layer_taunt_rps_paper_lose.smd" animation file shows what we would expect, the taunt animation.

The other two animations you mentioned probably have the same setup.

In conclusion, this is not a bug in Blender Source Tools, but a bug in Crowbar (because of the lack of data in the SMD file, which should probably be an idle animation that is combined with the layer animation).

The problem is likely the decompiler did not create the animation files correctly.

At some point, Crowbar will also convert between different SMD formats.

This issue was discussed here:
http://psteamcommunity.yuanyoumao.com/groups/BlenderSourceTools/discussions/1/615085406664476485/

A modder could simply rename the materials in the SMD files and add in the folders in $CDMaterials lines.

No evidence has been provided. Not even a bug report.

It is a problem with BleST.

Hmm, how odd. You should report the details of the issue in the Crowbar steam group.

This is a bug with Blender Source Tools because it is valid syntax for the studiomdl.exe compiler. I made Crowbar list all options inside the braces for $sequence to make it look better. It seems though that many people are used to the old way of listing $sequence options, so I'll probably include the old way into Crowbar's "Format for stricter importers" option. :S

This seems to me an issue with understanding Blender's interface. The VMT (material) names found in SMD files are in the Material (gasp!) property pane as shown in this image[34c89b82-a-62cb3a1a-s-sites.googlegroups.com]