Hello, Circle Dock will automatically overflow into multiple concentric circles when the inner circles fill up. You can change the number of icons to put in a circle by going to Settings -> Dock Shape

Circle Dock uses a mouse hook to capture the middle mouse button so it would see the button down event before your remote desktop application. To work around this, you can temporarily suspend the mouse hooking in the current computer you are using by right-clicking on the middle of the dock and checking off "Disable Mouse Toggling". This will stop the mouse toggling on your current computer and allow your remote desktop program to see the middle mouse click. To restart the mouse hooking on your current computer, right-click on tray icon for Circle Dock and select "Enable Mouse Toggling"

Hmm, there shouldn't be any change in the performance of opening a program through Circle Dock since there wasn't that much code change. However, if you are having problems with Alpha 8.2, feel free to go back to Alpha 8.1 since there isn't much difference. You can copy your settings back and forth between the versions without problems.