It is a bit of bizarre behaviour, imo (which is why I'm using Openbox now), but from what I read while investigating the "is it me or is it Fluxbox" question, I found that the issue is not so much that the windows disappear, as that they disappear from all other desktops than the one you opened it on, or something. So if you switch to the desktop you opened it on, it will appear as minimized in the taskbar, but not on the taskbar of any other desktops, even if you have "show windows from all workspaces" set (which, as far as I know, I do).
This did seem to work properly under 0.9.9, but does not seem to work (or has changed behaviour so radically as makes no never-mind) under 0.1.14.
Hope this helps.
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