I did as DJCB suggested and deleted the .mu dir. I also updated all my packages. The problem persists. I wonder if it's really a contacts problem.
In the last message in the thread you refer to, Chris Boo says he sees the error in Ubuntu 14.10 but not in 14.04 which he thought meant a bug was introduced.
I can see that you tried to reproduce the problem, it seems like you were manually fabricating the mail messages but I'm not sure.
It looked like you were trying to prove that the secondary addresses were making it into the database.
Do I assume the search query is going direct to Xapian?
I suppose this is not a super common problem for people so it may not come up much.
I think there's a bug but I'm not sure where. I'm still fairly new to elisp but I'd be willing to have a look if I had a clue where to look.