This is definitely not a limitation of X.

Almost all tray icons work fine, including ones I have authored myself.
A few that stick around are GL Desktop, Nut client, and Mail-
Notification.

In GTK terms, the tray widget is given a delete signal when the tray is
restarted. Returning false from this signal forces the widget to stick
around. When the tray restarts the widget/icon is still present and
shown.

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Tray icon is lost when tray is restarted
https://bugs.launchpad.net/bugs/176169
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