I use relative paths too (it's more easy to clone a project then). It broke for me with VS2005 SP1 (unfortunately upgrading to SP2 is blocked by the environment of another project the is built with it) on 32bit Win XP as well as with VS2008 with all SPs and patches on 64bit Vista. It's really strange.
As a workaround, I just imported the .pro files again. That would be suboptimal, but doable. But unfortunately, the make dependencies are messed up seriously. I rebuild the whole solution, then hit F7 and the every single project is rebuilt completely again where it's supposed to do nothing.
I gave up on this for now and switched to Qt Creator using the VS toolchain(s). My statement from the initial post has to be revised so far :-)