The System Preferences application on Mac is universal since Snow Leopard: it can run in 32-bit or 64-bit but not at the same time. That's why you have to restart the application when you want to open an older Preference Pane.
Today I tried to upgrade the LazyPoken prefpane as it was still a 32-bit build and the next Mac OS X will probably no longer support the 32-bit System Preferences application. That turned out to be a little harder as expected.
First of all you should change your project ARCH flags to tell the gcc compiler it should build for 64-bit. You can do this in Project → Edit Project Settings, choose the Build tab and look for the Architectures or ARCHS parameter. Choose the 64-bit or Universal mode (if you need to support Tiger).
This is not enough however. If you try to build and install your application you'll notice it's still running in 32-bit, stubborn prefpane.
The 64-bit System Preferences application also uses garbage collection and all 64-bit prefpanes need to support this as well. You can enable this in the same build panel under the Objective-C Garbage Collection or GCC_ENABLE_OBJC_GC parameter. Choose the Supported or Required option, again, depending on what you want to support.
Clean and build your application again, check for warnings and try it out. Looking better now?
- Sparkle: make sure to include the With Garbage Collection version of Sparkle, you just activated garbage collection remember?
- Older frameworks: make sure the frameworks your application depends on compile in 64-bit mode. The Developer Tools installed with Xcode include a tool to check your code for possible 64-bit incompatibilities. Read the Converting an Existing Application to 64-Bit documentation.
Still running into problems? Read the Updating Preference Panes for Snow Leopard and Beyond article from Apple's Preference Pane Programming Guide.