I thought it just something I was doing. Then someone emailed me about about the same issue. Then I checked a user that I set up on ArcGIS 10 and his had been wiped.
It doesn't happen right away--days go by before the AddInFolder XML tags in the AddInFolders.xml are removed for no apparent reason.
Is this a regular occurrence? A documented bug? User error?
I've checked set Read-only attribute on the file, so hopefully that makes it stick. But users can't add Add-In folders (not necessarily a bad thing for me).