Issue w/ Latest Stable vs. Latest Nightly

I am converting our company VSS db (500MB) to SVN (duh).

I ran a test run w/ the Latest stable and ran into the "Archive Project" issue. (puts all restored projects into the orphaned folder).

I ran a second run w/ the latest nightly and the data is in considerably worse shape. Many files are now no longer the latest version and are placed into the SVN repository as latest when really they are years old.

Any ideas?