Thanks for the report, crlundy!
The end-of-phase/beginning of phase thing is sure getting more important, as more and more cards use it. I had a similiar few minutes of confusion when I played Pirate Ship, attacked and actually got some Gold in addition to the pirate counter. In the log it totally looked like it was part of the Pirate Ship effect.
In reality, it was Gold from the Treasure Chest. It just made perfect narrative sense that a Pirate Ship would bring you Gold, so I had to look at the text again to make sure I didn't misremember.
About the Coffers use before the gain: This is probably confusing, I'll see if something can be done about it.
Again, thanks for reportin the problems!