I don't usually pay too much attention to those download time estimates, since they're usually not accurate. Once the download gets going, everything sorts itself out.

It's possible that your problem is being caused by those two files, although downloads will usually replace any existing files with the same name (but I haven't spent a lot of time with Vista yet). Have you tried rebooting to see if Vista simply has those files locked? I'm not running the Microsoft security trial (I'm using Symantec), so that's different from your setup, too.