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I don't see such thing with ksh93 in urxvt.(about parts of the command line disappearing)
I'm not sure from mind what causes this, come to think of it I suppose it could also be an effect of setting up a specific prompt...
[USER=38324]ShelLuser[/USER] , since you use Xorg, have you tried running
resizewhen such things happen?
I noticed that sometimes terminals get screwed up by "bad outputs" of certain commands.