I have no idea if your problem is the same, but a few years ago i migrated a site from EPiServer 4 to EPiServer 5 and have a similar issue. The solution was to disable WindowsMembershipProvider and WindowsRoleProvider for the site and enable SQLServerMembershipProvider and SQLServerRoleProvider.
my client have node in the page tree from their old intranet (EPiServer 184.108.40.2063) and they want to export it together with linked files. The export takes forever and I get prompted several times to log on (window authentication) but the end result is always the same. After around trying to export for like 10-15 minutes, an error page comes up and says "You are not authorized to view this page". The weird thing is that when I export each subnode just below the page, it works fine. The conclusion I can draw from this is that the export file is either too big or takes too long to generate so that the session times out.
When I've exported all subnodes and calculate the size it sums up to around 800-900 MB.
My question is this: What settings can apply to the website to make this work? I have set debug to true so that executionTimeout shouldn't be a problem and I've set the maxRequestLenght to around 2 GB.
The site isn't in use so it does't matter if it requires a setting that isn't safe or not recommended for some reason.