I have downloaded the bowtie tools 0.12.9 from the site of the project. They do not work on Mac OS 10.6 (both 32 and 64 bits). If you run bowtie or bowtie-build then you receive a message: "Unexpected block: 4".
The version 0.12.7 works well. I have tried to build the 0.12.9 version from the source code and they works well too. Could you investigate and fix the problem, please?