I get the same error - "Your Quicken program files (not your data files ) may have been damaged. You will need to reinstall Quicken." - also running QPHAB 2006. I've tried on Suse 9.3, Suse 10.0, and most recently Kubuntu 5.10. I've tried starting installation from the Configuration window, and from the Crossover/Install Windows Software menu item. I've tried letting the autorun do the installation, and I've tried installing as unsupported by browsing to the install.exe app on the CD. I tried installing IE (web download) before I installed Quicken, and I tried letting the Quicken installer install IE from the CD as part of the Quicken install. I tried using the default bottle, and I've tried making a new one (Win 98). I'm baffled. All of these got the same error message when I tried running Quicken.
What's really frustrating is somehow I got QPHAB 2006 running perfectly on CXO 4.2rc2 on Suse 9.2, and I can't remember what I did. Registration and everything worked. (Interestingly enough, and maybe this is a clue - when I upgraded my working 4.2 installation to CXO 5.0.1, I got the same error again. So 5 is doing something that 4.2 didn't, and it seems to be breaking Quicken, at least it did for me.)
Some people are getting it to run and others aren't. It's a puzzle, for sure.