Martin

I am attaching a patch that should fix this issue. I will let Nicolas
review/apply it.

ps: If you are not comfortable applying patches, the best way to get
things working again, is to force a blank line before the first
non-commented line in your Org file i.e., replace

--8<---------------cut here---------------start------------->8---
[snip]
#+XSLT:
* Protocol
--8<---------------cut here---------------end--------------->8---

with 

--8<---------------cut here---------------start------------->8---
[snip]
#+XSLT:

* Protocol
--8<---------------cut here---------------end--------------->8---

in the test file that you circulated.