Make sure to use the latest code from Subversion, rather than 1.7. I think there have been changes here.
I see output that begins like FNC0103453 ...
This seems correct. Why do you expect FNC1010103453 ...? that is, where is the extra "101" coming from?
I think the contents are being read correctly. I don't know if FNC1 has special meaning in GS1, but it is not further translated. I can tell you that it is definitely rendered as ASCII 29 though.
So, perhaps you would just need to further interpret the results in your app.