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).
Best Answer
So this is the culprit. It's a far more likely reason than the answer I posted yesterday (also reproducible, but not easily).
"NIM060555: ArcMap Add-ins stored on a network drive does not persist if ArcCatalog is opened between ArcMap sessions".
I was able to reproduce several times.
The work around of setting the read-only attribute on the AddInFoldersList.xml works, but user can't add/remove folders while in ArcMap.
Steps to reproduce: