In 4.0.1 Beta 7, applications with those options described in the subject, do not behave properly.
In the Taskbar options, if I have it set to "All taskbars show relevant windows," these applications will minimize to the windows default taskbar and won't hide properly in the system tray if they are on my secondary monitor. If I use either of the other two options, they work fine.

The two apps that are doing this right now are Outlook 2010 and Lync 2010.

This is the first version that I've noticed this happening in, although I just upgraded from 4.0.1 to Beta 7 today.