Thanks for the tip jsmcms!
Franco, Since you reported connection success with the n32 64 bit serial driver, I went ahead and uninstalled the current VISA drivers (there's an uninstall.txt file in the National Instruments folder that describes this) and installed the 64 bit VISA drivers. All went well, tested 2560, and the Mini, but guess what, the Mini stops before it gets to the upload process. I'm willing to bet I missed something when I was making fixes for the issues that MikeD was reporting. I think I can fix it fast and will release a v3.0.1. If you have time, please look out for it and we can nail down all the Configurator issues with the Mac.
If there are any others seeing MikeD's problem, please let us know and if you can identify anything that can help us diagnose it.
I think the real way to fix this is to mod the avrdude.exe file like JesseJay has suggested. JesseJay and MikeD, how do you go about compiling the changes made to avrdude? A straight make didn't work, it looks like it uses some automake stuff, I started reading up about it, but didn't have time to continue learning about it. I'd like to see if we can make a Windows and a Mac version. THANKS!