The new ArcGIS 10.x LM serves license authorizations to ArcGIS 9.x clients.
No issues other than an ArcGIS 9.3.1 client can not be served Bing Maps/Virtual Earth license authorizations via an ArcGIS 10.x LM, so if continued 9.3.1 use of Bing Maps is an issue--retain an ArcGIS 9.x LM as an alternate license pool.
Once installed, the ArcGIS 9.3.1 SP2 does resolve Desktop Administrator issues when polling the ArcGIS 10.x LM. But as you mention some folks have had problems with the download and installation. But, that was not our experience and may just have been load on ESRI's download servers when the patches were first released.
Stuart