Cisco VPN client is known to change the interface’s MTU. In doing this it should connect, however, it will lose connectivity. Default MTU is 1500
http://www.pctools.com/guides/registry/detail/280/
VMWare Workstation 6.x some combination of bridge/nat interfaces (IME 1 of each) will prevent Winbox from connecting via MAC. You will see the CDP broadcasts from your MT but you will not get a response from your Winbox’s request nor will you be able to connect.
Disabling all VMWare interfaces in ncpa.cpl worked for me.
This thread suggests Macromedia changes the profile for storing addresses
http://forum.mikrotik.com/t/winbox-running-on-windows-vista/13378/1