It is reproducable, but I'm afraid not 100%.
1) Make sure your 'Window List Preferences' have 'Window List Content'
set to 'Show windows from current workspace'
2) Start opening windows. I was able to reproduce this problem with just
Firefix and Console windows. Watch the Window List. At some point, it
suddenly all windows disappear from the list.
3) Toggle your 'Window List Content' between the two settings and watch
all windows (dis)appear from the Window List.
** Changed in: libwnck (Ubuntu)
Status: Incomplete => New
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Window List sometimes mixes up windows from different workspaces
https://bugs.launchpad.net/bugs/290339
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