I don't know if this is considered a bug or by design (reported in hydrogenaudio forum), but it seems undesirable--gapless tag info is silently removed when replacing all tags. Perhaps gapless tag info should be considered part of the data, not metadata. (like "filelength" or "bitrate", it makes little sense to delete it or replace it except as part of the encoding process, at least not without user confirmation or special non-default option box checked):

gapless tag removal

I just wanted to let you know that I've read your report and will think of a solution to this issue.

Thank you (as an enhancement, please also consider adding a utility to create the itunes gapless info tags without re-encoding the file--itunes has that capability).