Jon, if you're reading this forum, can you look at the known issues you added from 2.1.0 and see if you still have them? Except for the one where I worked around it by disabling ntpd, I haven't seen those happen with 3.0.0 and the latest game version, and I've been pla^H^H^Htesting a fair bit.
Also, I haven't played this on Windows in a very long time (over a year) but I seem to remember sometimes there it could take a long time to load as well, and sometimes I would have to click on game objects multiple times for it to register. Now I'm tempted to go find a Windows machine and see what it does if I adjust the system clock while the game is running.
One thing I know from the log files is that recent versions of the game try to change the cursor to an animated icon while it's loading so the user gets some feedback, and those API calls are not yet supported in Wine.