If you go to
http://forge.ocamlcore.org/projects/irextools/, you can download version 0.1 of my portable (Linux, certainly Mac and likely also Windows) scribble merger. There are also some file management utilities in progress.
In this version, I have replaced the baroque algorithm for determining the zoom factor (which was nevertheless not always right

) by the zoom factor stored in the metadata.db file. This appears to work reliably. [The baroque algorithm was born before iRex released the source code and I didn't know where the zoom was stored - and I hung onto it for too long

].
I've never used iRex' official Windows scribble merger, but from the comments I read here, I'm confident that mine is not much worse

.
Please be advised that this is a source release and you have to compile yourself (see the file INSTALL). This should be straightforward for all Linux users. For the benefit of the Mac and Windows crowd, I would be happy if someone prepared binary distributions.
Have fun!