Thanks vitamin. $WINEPREFIX doesn't seem to be defined on my system but I think I've figured out what's happening. The path to Crossover's version of wine is earlier (in my path) than Wine's version. Therefore, when I double-click on regedit.exe, no matter which version of regedit I click, it gets opened by Crossover. If I explicitly specify Wine by typing this at a command line:- /usr/bin/wine regedit.exe then I get the expected (i.e. wine) version of the registry.
