I have been talking to the autopackage developers about 64-bit support and basically autopackage is untested on that platform. I built a package on my 64-bit machine where I'm running all 64-bit libs and the result was that it failed to find most of the libraries, because of the problems like yours - the libs are in a different place (lib64 instead of lib) and thus the autopackage skeleton system can't find them. I may be able to come up with a way to use manual library checks to find the libs instead of the skeleton system; unfortunately this has some drawbacks like all the messages will only be in English, it will not take advantage of autopackage's very extensive translations. Anyway the 32-bit version will probably not run properly on a system with all 64-bit libraries.
That's the long answer.
The short answer is, I'll try to have a 64-bit package together soon. I'll keep you posted on the progress.