Hi @dwa, I’m a big user of Parcellite so had to look into this. I’m assuming you’re running 17.10 which I have in a virtual machine. I’ve been using Parcellite in 16.04 all along.
But in 17.10 I discovered the Parcellite icon seems fine in my “Traditional” panel Notification Area but once I started trying other panel layouts in MATE Tweak the symptom appeared just as you describe. Unfortunately, so did instability, corruption and crashes. I’m not sure if the Parcellite icon was a factor but it seems to be a catalyst.
@Wimpy has been busy looking into panel switching for 18.04 and reports a lot of debugging has been done. Maybe we can get him to look into this but his work won’t get to 17.10 for awhile, unfortunately.