Kyprianos,
All I know about software, is that the versions MUST match (IE 9.1 ISE +
9.1 EDK is OK, but 9.1 ISE + 9.2 EDK IS NOT OK!).
Yes, Virtex 5 has been out for 18 months now, with the LX, LXT, SXT all in production, so there are even older versions (ie 8.x) that support V5, and hence, partial reconfiguration.
I always recommend starting any new project with the latest release of software so as to take advantage of all of the bug fixes (without having to load service packs).
The next best choice is to use the immediate previous version, with all service packs. This is just the "way of software" and really has nothing to do with Xilinx: the latest version inevitably has some new bugs, and the immediate previous version is usually the best possible choice for software that has the fewest unknown, or unfixed behaviors.
The newest version has all the resources going to fix things in the shortest time. The previous version has had perhaps 100,000 users banging on it for 6 months or more.
Austin