I have two bootable OS X partitions on my Mac. How do I keep the settings and applications from one partition from leaking over into the other?

For instance, default file-associations frequently mix and sometimes preferences are even overwritten.

Disabling spotlight indexing on the partitions does not fix the problem.

The only solution I've found is completely unmounting the partition; however, that restricts me from accessing that partition's filea. Is there a "softer" fix?

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