I've installed biber on both 32- and 64-bit versions of Ubuntu in essentially the same way you described with no problems, although I put the extracted biber in /usr/local/bin. The error you describe sounds strange, though. What happens if you run (say):
/usr/bin/cal
..?
If that works as expected, then I'd delete older versions of biber, extract a new copy, make it executable, and try this sequence:
- first: make sure
backend=biber is an option you're giving to biblatex;
- run your file (my_paper.tex) through (say)
latex (this should create a file with a .bcf extension);
- then run
biber my_paper or biber my_paper.bcf (not biber my_paper.aux).
If you're having trouble with these steps, then can you even run biber -v to check your version. (I get biber version: 0.9.6 (beta) when I run the command.)
Another thing to check is that your biblatex and its related packages (etoolbox, logreq, and, ideally, csquotes) are also up to date --- although I can't see how this could relate to the more profound error you seem to be experiencing.
EDIT: you may want to look at the biber documentation as well:
http://sourceforge.net/projects/biblatex-biber/files/biblatex-biber/development/documentation/