There is a forum for Memoria at GOG herehttp://www.gog.com/forum/memoria
though it doesn't look like many people post there.
Someone seems to have a similar problem to yours herehttp://www.gog.com/forum/memoria/bug_with_messenger_chapter_vi
They say it's a known issue and Daedalic is working on a patch. Apparently the bug is triggered by the order you do things and can be avoided (if you know what not to do ahead of time).
This is a known issue and Daedalic is currently working on a patch. I am not sure when they will release and if it will work straight away with gog's version.
The easiest way to prevent this bug from happening is to talk to the messenger only after you talked to the guy in bog and then send the messenger to the bog. Just make sure he can't cross the river or the bug will occur. Once you got the scroll you can finish the game without any bugs.