I have had this problem now with two apps, they both use the
libappindicator to display their indicator icons (I believe). First time I had this problem was with
Ubuntuone-indicator app, now I have this same problem with Sparkleshare, so I figure it must be related. I just recompiled and installed sparkleshare 1.0 from source last night, thought that might be the problem. Still same thing.
All works fine in Gnome, but once I go into XFCE it give me the missing icon problem. Could it be as simple as an icon out of place? If so where do I move the icons to?