If you want to take advantage of all the out of the box features and allow your upgrades to go much smoother (along with about 100 other reasons), you should choose a Blank Portal site. If you start off with Portal, you can always add ASPX later. But you can't go backwards that easy.
When you do your install, are you doing a vanilla install of v6 or v7 then run the site, then apply the hotfix up to 42 or 58? After every fresh install, hotfix, or upgrade, you need to run the site. You might also try to download the latest .exe from the DevNet and see about running a fresh install of the program files or upgrading your program files.