After installing TortoiseSVN 1.6.0, all files loaded into an AnkhSVN enabled Visual Studio 2008 project are marked as new (blue +).
I have tried re-installing AnkhSVN 2.
Sadly this solution does not work for anyone using VS2003 since there is no daily build (SVN 1.6) for the 1.x branch of AnkhSVN.
The AnkhSVN team has stated that they are too busy right now to update AnkhSVN 1.x (ie the VS2002/VS2003 version), so it looks like unless someone is willing to help them with it (it’s open-source), there may not be an SVN1.6 version for VS2003 for a while.