I figured it out.
So I tried various versions 5.3.2 / 5.3.3 etc and nothing was working for me.
The program would happily install but would not run when I tried to launch it.
It would seem that the program has some dependencies it requires that it doesn't bother to check for from what I can tell. luckily these are easy to obtain although I've not been able to specifically identify them (lack of time).
The simple fix is to just install something like Wine and this will have packet tracer loading up (not in Wine before you think I'm cheating!) in no time.
I've created a bug report but it looked like there were similar reports for other versions of Linux and also they have some newer revisions of Packet Tracer in the pipeline which will hopefully remedy this.
http://ptbugs.ptnetacad.net/bugzilla/show_bug.cgi?id=10628
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