Sometimes saving brings up an error.

[micheus]

ptoing, does that wings file causing the error you were experiencing?
I played with it, used save, save as,... and nothing.

I used Wings3d 2.0.5 (that appears in your dump log above) and your preferences file.

Do you have used someday the option "File->Save Preferences Subset..."? If you did that, you may have hotkey data stored in a subset of preferences that is stored in the same place as Preferences.txt file, but with the extension .pref.
I noticed in your preferences file a reference to other file:
{pref_directory,"c:/Users/ptoing/AppData/Roaming/Wings3D/backup_prefs.txt"}

The renumber issue is something that appears here sometime and use to be related to malformed mesh. You can see a sample of this here.
It's hard to discover what is happening if I can't reproduce it in my PC.

As you are using (very) old version aside with the current one, I would suggest you to change Wings3D 2.0.5 shortcut (or create a new one) pointing to a different place where it should store/load its preferences file - like this:
"C:\Program Files\wings3d_2.0.5\bin\werl.exe" -run wings start_halt -extra "c:\temp"
in which "c:\temp" is a folder where the subfolder Wings3D will be created and the new preferences.txt stored.
It will bring back the Erlang console, but I don't think that it would be a problem.
If the hotkey issue is related to the many version sharing the preferences file, then this can avoid that.