I found a solution.
The problem is that when the architecture is not specified Snow Leopard defaults to 64-bit, while older versions of the OS default to 32-bit. In the Poco build system, the Darwin config file does not specify the architecture, so it picks 64 bit.
My solution was to copy the Darwin_x86_64 config file over the Darwin file and replace the textual instances of 'x86_64' with 'i386'. This forces a 32 bit build.
A somewhat hackish solution though, let me know if it can be done in a cleaner way...