Yes, the source code on that site seems to be not the newest one. This is also something which fits within the comments I made above. If you see a loss of some functionality of my version of the djvu file viewer it certainly is because I had not the original source code available.
I worry that the same is true in the case of FBreader. Have you checked out the subversion version at this url:
https://pocketbook-free.svn.sourcefo...er-pocketbook/
Alternatively you might just use graynm's source code at:
http://code.google.com/p/fbreader-po...ource/checkout
This is not the sourcecode for fbreader but fbreader180 but it is in active development.
Sorry, that I couldn't be of much help.