It sounds like an up axis is incorrect somewhere, possibly you are importing an animation made with one model in SFM onto a different model in Blender.

It's a check box in the list of installed Blender add-ons.

It looks like another script within Blender has messed with the console window, and replaced a key component with its own "StdoutOverride". Try disabling other add-ons until the problem goes away.

This is a Blender issue. Nothing an add-on can do about it.

The file is broken. Both meshes have data for four joints, but only two joints exist.

Pupils are rendered entirely by a shader. They don't exist on the model, you just tell the shader where the eyeball is.

It's not a recognised game, surprisingly enough. I never added it. Do you know which version of Source it runs on?

It's not a registered game/engine release in the tools. Apparently it's based on Source 2013, which means that it wants DMX encoding 2 and model format 1.

You can enter these values manually, please let me know if they work. I'll add them.

Fixed in 3.2.6

No issues here. Are you looking in the right location? You can open the console window to see exactly which file paths are being written.