Hello,
I can confirm the issue with the Finder sidebar icon on the latest 10.11.1 beta. As we haven't changed anything in our code related to it, my best guess is that it's a bug in the latest beta - but we will keep an eye on it. Thanks for the hint.
Regarding the other problems: Would you be so kind and create a debug log for me? Here's the guide how to create one:
https://support.boxcryptor.com/display/BCOSXEN/How+to+create+a+Debug+log
Best,
Robert