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I'm not aware of known issues, however, it would be best to check the Microsoft KB articles for any patches that were deployed to that machine to check for known issues.
I don't think this is new behavior. I did a test install of Office 2007 with no patches or service packs and the same thing happens. I pushed one non-Office patch (flash) with immediate reboot. Excel asked if the spreadsheet should be saved; I didn't respond. The recovery file disappeared about the same time as safereboot killed Excel.
If I kill Excel with task manager, it goes away without prompting to save modified files and the recovery files are not deleted.
As a workaround, we're going to move the recovery files to NetApp disks so there will be snapshots that can be restored.