What i did:

Installed dnn, no probs
i was playing around with the export/import function, importing a portal.
i read on some site that it helped against broken links to /Portals/{PortalID} folders if you specified the portalroot explicitly.
Now the html for the logo looks like this
<img style="border-width: 0px;" alt="portalname" src="//portals/HOV/HOV.jpg" id="dnn_dnnLOGO_imgLogo">

double // is all that breaks it.

I think I added a / while specifying the portal home directory I should have chosen "Portals/HOV" instead of "/Portals/HOV"

 On a working DNN installation do the following:
Click :
Host->Portals
 Add new portal
next to "home directory" click customize
Enter the path to the Portal home dir, in my case "/Portals/HOV"
finish it and click on "create portal"
 Dotnetnuke creates the /Portals/HOV directory

 The problem is created.

Now if you go to
 Admin->sitesettings
 expand Appearance
The top item is logo
 It shows "Portal root" as folder and you can select a file from the portal homedir but it doesnt work as supposed to