We are having an intermittent issue with permissions at the Site Level being completely removed. The Groups and Users at the site collection level are not affected. The following description: We have a document library in which the documents have had their inheritance broken from the parent site. This is required as each document is being updated by a different user with "Approve" permissions. Three times now he has placed specific permissions on each document, both individual users and groups. Both web service calls to GetGroupCollectionFromWeb and GetUserCollectionFromWeb then list the users which have been specified. At some point while the user is specifying permissions the site would experience some sort of event where the site would stop honoring the webparts and links on the site which are controlled by Audience. I then go to SiteActions/SiteSettings/People and Groups/Settings/Set Up Groups and do nothing more than press Enter. At this point the Audience then works. However, we then see that all the work which has been done to specify individual permissions on the documents are gone. Has anyone experienced this and have a possible cause and solution? If this is the wrong forum please let me know.

Problem solved... The new site collection administrator was breaking inheritence on the groups and users when he should have not have been. User error.