Shell integration breaks multi-line prompt in fish shell

• iTerm2 version: Build 2.9.20160206
• OS version: 10.11.3 (15D21)
• com.googlecode.iterm2.plist here
• debug log (debuglog.txt)

I use a double-lined custom prompt with my fish shell and it seems that the new shell integration, with its extensions to the prompt, breaks the double line and flattens it out into a single line.

I'm attaching a screenshots showing the process from the "before" to the "after".