Have also seen a few guild members have this problem. It seems to be the same one or two, so maybe it has something to do with their browser setting or something like that.

I did loose 5 gems the other day sailing. I jumped onto a ship then off, as I jumped off a guildmate clicked on. That bugged my display and I didn't appear to be sailing and the envelope didn't appear. Refreshed browser but my gem count didn't increase and the packet didn't show up. Did get credit for a successful sail however.