We left both versions running on our clients at the time of our initial upgrade (to ensure compatibility) with no issue. (We were having some XP/Win7 issues at the time, unrelated to Arbortext itself). We're completely on 6 now, however.
I'd still caution that FLEX is a little wonky when it comes to which mac address gets used, so be sure to choose wisely, especially if your users have laptops and are accustomed to going between docked and non-docked/wifi profiles, as FLEX will fail if the adapter is not present. We've found that the default Win7 setting (at least for our machines) is to disable the ethernet adaper when not in use... something we were able to change in the power profile.
Also, FLEX will not work over a terminal services session.