I suppose you have found your answer to this post, but just in case you haven't, I had this same problem recently and I found the answer at www.aspsmith.com IBS Portal Bugs/Upgrades under:
Q: BUG FIX: When I deploy to a root web, how do I get my links to work correctly (Request.ApplicationPath doesn't work)
This fix was also recommended by others who responded to my post for help.
I tried it and it worked perfectly...although it does require some time to make all the modifications.
Regards,
Mike Parks