Hi, after a lot of mucking around and starting a conversation with the creator of MagicPrefs (see here) and following his suggestion to use fs_usage to monitor, my next suspicion is the Mail app.
These are the unlink calls that generally precede the GlobalPreferences.plist file disappearing from my Library/Preferences.
09:20:26.435 unlink [ 2] /Users/jetset/Library/Preferences/.GlobalPreferences.plist 0.000004 Mail
09:20:41.436 unlink [ 2] /Users/jetset/Library/Preferences/.GlobalPreferences.plist 0.000004 Mail
09:20:56.436 unlink [ 2] /Users/jetset/Library/Preferences/.GlobalPreferences.plist 0.000003 Mail
The two bundles I have installed are GPGMail and MailFollowUp. Anyone else running Mail with these bundles? It's also possible that it's a weird bug in Mail that's deleting GlobalPreferences, but that's much more unlikely because then almost everyone using it would be experiencing this issue.