The Macintosh recently moved to using Intel CPUs instead of the IBM PowerPC ones that they previously had. To make this transition smoother, Apple implemented a software emulation layer called 'Rosetta'. So now Apple has two ways of labelling applications:
'Universal' - applications that will run natively on both PowerPC and Intel CPUs, at full speed.
'PowerPC' - appllications that will run natively on the PowerPC, but emulated on the Intel CPU.
When I build a JAVA app using Advanced Installer, it is built as a PowerPC application, meaning that it will actually run slower on the new Intel machines, because it will run in the Rosetta emulation layer.
When I use the JAR Bundler that comes with Xcode on the Mac, they are built as Universal Binaries, meaning that they will run at full speed on both Intel and PowerPC platforms.
I think you guys just need to update whatever library it is that you're using to build Mac Apps, and you should be able to build Universal Binaries.
More information:
http://www.apple.com/universal/
http://en.wikipedia.org/wiki/Universal_binary