This problem was introduced by the fix for 6485081 in 6u4 b03.
In that fix, we no longer copy our javacpl.cpl into the windows system32 directory in order to avoid the Program Compatibility Assistance (PCA) dialog upon exiting the Java Control Panel. That fix also creates javacpl.exe and registers it accroding to MSDN documentation. Apparently, it doesn't work well on Vista 64-bit.
This fix places the 32-bit Java Control Panel icon under the "View 32-bit items" area of windows control panel on a 64-bit Vista machine. The fix is suggested by a Microsoft support engineer who has also filed a MSDN documentation bug after this investigation. Currently, this solution isn't described in MSDN yet.
The registry key which makes the difference is:
(Note the "WOW64" appended to "ControlPanel")
Tested the co-existence of both 32-bit and 64-bit Java Control Panel.
Also tested when both 32-bit and 64-bit JREs are on the same machine, uninstalling one JRE doesn't remove the Java Control Panel for the other.