In Xfce 4.6 and Orage 4.8.3, I notice of that systray icon briefly disappears and immediately re-appears quite often. Perhaps this happens at every resume from suspend, but I notice the same issue at other times. Unfortunately I seem unable to find any consistent behaviour. With "Use wakeup timer" on or off, the icon doesn't systematically disappear/reappear when resuming from Suspend. But I still notice the systray icon disappearing/reappearing at times. Another symptom of this issue is I see a similar issue with Xfce 4.8 and Orage 4.8.3: When I resume from suspend I sometimes get two Orage icons in the systray (using "Use wakeup timer" on). I suspect that the behaviour that I reported above---systray icon disappearing/reappearing at times---is slightly modified in this case, namely the 'disappearing' of the icon no longer happens so I end with two tray icons of Orage. Right-click on any of the two and Quit will make both icons disappear. Perhaps this is a panel/systray issue?
I really would need a reproducible case for this.
I have not seen this for a long time. Please, reopen if you can still see this. That two icon issue is very probably panel/systray issue as I never saw that with gnome panel. I assume that also is fixed now in Xfce as I have not seen either for a long time.