Sorry for the very late reply on this (I've been extremely busy lately). Are you still having issues? I've been running 4.6.x just fine on CX12.x (now on 12.2 with Ubuntu 13.04).
Have you looked through the tips & tricks to see if any of those points help?
There are issues with crashes on start-up. The usual symptom is that the process runs on high CPU (shows 300% for me!). When this happens you need to kill the bottle. Sadly for whatever reason, Codeweavers removed the bottle reset link. To use it, run "/opt/cxoffice/bin/cxreset". I've simply created a Unity shortcut for it.
Once you have killed the process, just try again. Sometimes it can take a few tries to get it running. I've raised this issue with codeweavers but I don't think they will try to fix it.
For what it's worth. I have MS Office installed in the same bottle. Before I start Evernote if I start an office app (like word), Evernote usually fires up without an issue. Perhaps running the other app starts some libraries not loaded when evernote starts fresh???
UPDATE: After I upgraded to 4.6.6xxx, 9 out of 10 times the application would crash on start. I do not recommend this version. Go to file hippo and grab the older 4.6.4xxx. Also I was told that the Crossover developers recommend running each application in there own bottle. I tried this with 4.6.4xxx and it works pretty well.