Subtitles not synchronized ?.

[Woodstock]

Subtitles have time stamps for their start and end (some use start and duration rather than end time). Something is screwing around with that timing in your workflow.

Are they synchronized when you play the original MKV file?

[Chetwood]

You're manually adding a subtitle track that is not on the BD? With matching framerates from the mkv and the BD you got the Italian sub from you can play the mkv with an external sub with VLC and adjust the offset to sync the subtitle to the audio. THEN mux it with mkvtoolnix adding the offset as the 'delay' under the track's format specific options.