Tried adding leading silence to an mp3 and stream copy didn't work as expected: the song was cut off after the 3000 ms I entered instead of a silence added of that length before the song.

yup, It not works for higher quality use re-encode instead

The third party tool used for the stream copy leading silence feature (OggCat) isn't compatible with all OGG files, so whenever it doesn't work, the best bet is using the re-encode option like Alex360 suggests.

Yep, always make sure re-encode is selected, had the same problem when the quality level got bumped up.