With Jwm it randomly dissappears and also the rox pinboard icons.Yesterday evening I tried to make a fresh new install on a USB key to try to solve two issues (this one on Conky an another on EZpup) on a 'clean' Xorg install. With Conky I had a partial success: if I use the default rc file installed by the pup file (with a black background) I have no flickers, while if I use the transparent one I was experimenting before I still have flickering. I had no time (I was too asleep!) to compare the two files, I suppose it should be a setting as trapster suggested: I'll let you know. But this is a proof that flickering and desktop content erasure can occur also with Xorg.
With xfce stable including rox icons inc transparent
mike