I noticed the following in xMaxima 5.12rc1 on Windows:
With plot preference embedded:
(%i6) plot2d(x,[x,0,1]);
<- embedded plot
(%i7) <- cursor jumps to this position but no input is accepted
(%o6)
1; <- first cursor position where input is accepted
(%o7) 1
(%i6) plot2d(x,[x,0,1])$
After the last input the only thing you can can do is to close xMaxima and start it again.
Volker