Hi Nicolas,
Thank you for reporting your difficulty on installing 3DNA on 64-bit Cygwin. It could be related to fact that the distributed version was compiled on 32-bit Windows. I will try to recompile 3DNA on a 64-bit Cygwin system soon. Alternatively, if source code is provided, did you know how to compile a C program? In a bash shell terminal, what happens if you type 'gcc'?
Back to you later.
Xiang-Jun