This is a tricky one... configure does have problems with cross-platform setups because it determines characteristics of the target by running small test programs. If host and target system differ, you run into problems.
An example (might not be completely correct but should show what's going on): the host platform is Win32, the target platform is Linux/ARM. Configure now wants to figure out what size a "short int" is. It compiles a small test program that basically prints "sizeof (short int)" and wants to run it. But this can't work because it would have to run on the target system.
It looks like you have to configure MAD manually, but that shouldn't be a big problem, it is really portable.
Eckhart