In Glines 1.0.51, if you click on a ball while another ball is moving, you trigger a bug which has a few different symptoms. First off, the moving ball stops without reaching its destination, but is effectively no longer there -- another ball that moves later may go through that space and annihilate it. The new ball you clicked on may go to its destination when you click somewhere, and all will be well, but usually it jumps to the upper-left-hand corner, annihiliating any ball already there. Once a ball jumps there, further attempts to play will cause balls you try to move to instead jump to that corner, until you run out of other balls (typical if you trigger this early in a game) or until something causes it to fix itself. In my experience, what causes it to fix itself has seemed erratic, but short straight moves and illegal moves tend to do this.
There is a new release of GNOME coming out in the next few days. Once it is out we will build rpms for rawhide and see if the bug is there or not.
jrb - take a look - I can't quite tell what the right situation should be
I'd close this one in the RH bugzilla, we've got it over in the gnome bugzilla. See http://bugzilla.gnome.org/show_bug.cgi?id=29791 for more information.
It's upstream.