It's most annoying, as RSSOwl minimises to the tray but hides its icon when you reopen it triggering this bug. And some quirk of how the icons have ended up in the tray means it's often the icon for Semagic that vanishes from my taskbar.
Anyway, the workaround is to not use the NIS_HIDDEN flag but instead just add/delete the icon. Or if there's just one application causing it then I think moving it to the bottom-right corner of the tray also solves this, as stuff in the last row seems to be reordered correctly.
I wonder how one goes about reporting bugs to Microsoft?