Prevent partitions from Spotlight indexing each other
System Preferences.. &gt; Spotlight &gt; Privacy
Add the mount path you don't want indexed to the list by selecting the device you want excluded also. However, if it's hidden use ⌘ +⇧+G and enter the path name for example /Volumes/Partition Y.


Note
After some testing this method does not work with multiple partitions of like OSs (eg. 10.8 on partition A and 10.8 on partition B) but does seem to work if each OS is different. Still not 100% clear on why this is since each drive has it's own /.Spotlight-V100/VolumeConfiguration.plist or /.Spotlight-V100/Store-V1/Exclusions.plist