I have half a dozen launcher icons on my panel, each for a single program. Every once in a while, the icons for these launchers disappear for a fraction of a second (the area where they should be turns to the solid gray used for the panel background). It's brief enough that it doesn't interfere with using the launchers, but it is noticeable enough to be distracting. I've also noticed that the panel and various out-of-process plugins write to the hard disk at 5 minute intervals, probably saving configuration. I speculate that the disappearing icons may occur at the same time, though I haven't verified this. Version of xfce4-panel is 4.8.5 (Arch Linux package).
The saving can be triggered manually with "xfce4-panel -s", but I doubt that is related.
I just tried running "xfce4-panel -s", and on the second try it made the icons flicker.
You were right, saving reconstructed the launcher icons. Fixed in 55783f5.
*** Bug 8072 has been marked as a duplicate of this bug. ***