You should press Exit to return directly to Pro Tools.  If you do need to save the preset, you may. However, you’ll need to return to Pro Tools, un-declare the Command|8 from the Setups>Peripherals menu, close it, then re-declare the unit.
This issue has been addressed, and a downloadable file is now available on the Digidesign Website. Please go to www.digidesign.com and download the file entitled “App V02.00.02.srec”. To update your unit:
1) find the C8FirmwareUpdater (located on the Pro Tools 6.4 installer disks) and copy it to your local drive.
2) Make sure the Command|8 is connected to your computer and powered on.
3) Launch the Updater and press the ‘Update Firmware’ button.
4) Navigate to the .srec file and click on it (the update process should begin automatically).
Once your unit is updated, the above workaround is no longer needed.