I have used GP5 (not 5.1) with ubuntu 6.06 before, with no dramas.
It was a bit sluggish to start, and load. But everything worked fine..
I used wine (windows emulator) to do it...
If Wine isnt already installed. Bring up a terminal
> sudo apt-get install wine
let it do its thang, and it should add wine into the "System Tools" Gnome window (assuming your using Gnome, im not sure about KDE or any others)..
From there you should be able to set up a "/wine/program files" etc and run the
guitar pro install and it should pretty much work straight off the bat. But i havent used it for a while, since i swapped over to Bianca (linuxMint, ubuntu 6.10 base)
From within the wine settings, there should be options for sound/graphics emulation. perhaps there settings in there are causing you your problems...
Let me know and ill see if i can help if you still have troubles....