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There's 2 possibilities here:

1) You have the 'archive previous version' box checked in the panel that appears when you update OmniFocus.

2) You're triggering the update install from a non-admin account, then authenticating to an admin account when the system does the install. We've got a bug in the updater that will always archive the previous version under those conditions.

(The numbers after OmniFocus are the build number, by the way.)