I'm trying out ZD v 2.0 beta 4 (zdesktop_2_0_beta4_b10514_macos_intel on Mac OSX 10.5.8). When I change the View to place the reading pane under the message list, then close ZD, reopening ZD reverts the reading pane position to the (default) right side again.
Same is true for expanding the folders tree under the Accounts pane at left. If I expand a Zimbra account folder tree, close ZD, reopening ZD reverts the display to just the account name and hides all folders under the account.
I'd expect these settings to be retained across closing/reopening sessions.