Altering a profile of VLC transcoder component (Convert / Save feature) that has no encapsulation set breaks it by enforcing the MPEG-TS encapsulation
I discovered this when I attempted to alter the Audio - MP3 profile; I wanted to change the audio sample rate to 22050. After saving the changes VLC tries to produce .TS files instead of MP3. This seams to be caused by the missing No encapsulation or None radio button in Encapsulation page which should be checked by default when it's the case. By saving that profile change I unintentionally enforced the MPEG-TS encapsulation to it, that's because it's the first option in encapsulation page. And because I am not aware of any way to reset transcoder profiles to factory state (resetting preferences and cache doesn't help) the only way to reset the profiles was to reinstall VLC.