What really needs to happen is for Kerry to release his FULL military record, so we can see who put him in for what medals, and ask those people the story. While he has released some snippets of his record, the whole thing is not there. There's enough proven shadiness on the part of the Kerry Campaign on Kerry's Vietnam service that I think it's legitimate to question other aspects as well.
As a Naval Officer, I'm inclined to believe that if so many of his fellow officers who were near enough to his boat to see his actions say he may not have adhered to the highest standards of Officer Like Conduct, that they may be on to something. While the guys on his boat liking him may mean he's a good guy, and he took care of his men, that's not exactly the same thing as doing your job as an Officer. In fact, at times it can be the exact opposite. Part of being a good Officer is going to bat for your guys, and they'll generally like it when you do this, but another part of it is making them do things that they need to but would rather not. For my part, I generally like command decisions that essentially benefit me in the short run, less work, go home early, etc. However, that doesn't necessarily mean I'm doing a good job of helping complete the mission. In other words it's highly possible that Kerry could have been very well-liked by his crew, but a crap Officer. Personally, how Kerry conducted himself after Vietnam is a much more important issue to me, and I think that those on the right that are questioning the medals are wasting their time on an unimportant issue, that's likely to never be cleared up satisfactorily.