I mentioned the Ubuntu version because, in principle, the DR1000 version
is the Linux Desktop version.
This seems to be a problem with iconv. The GNU version is supposed to include windows-1250 by default, so I'm not sure what the DR1000 is using.
If you want to fix this yourself, FBReader also includes a table lookup translation option. What might work is to add a windows-1250 file to the zlibrary/encodings directory. Use one of the existing files as a guide to the needed format and get the mapping to Unicode from one of the "external links" at
Windows-1250. I don't know for sure that this will work though.