Can't confirm this for an EeePC running ubuntu (Eeebuntu 2.0) and Wine (1.0.1). Minimizing works fine and so does restoring the window with 0.28.5 on this configuration, except the GUI being pretty slow; but I blame this on the Eee's hardware and as this is the first (and so far) only program I have run under Wine I cannot compare this to normal behaviour - but then, the GUI is even under XP ... let's call it different.
However when minimizing to tray, while the taskbar is hidden, the program is gone from the GUI (but running in the background). As being new to Linux I have to find out of how to bring it back into the UI (I killed the task and restartet, seemed to be the easiest way, even that I don't like that).