Same problem as in bug #3427476 here (I was unable to add a comment there, sorry). My configuration: Win 7 x32 SP1 Intel Graphics card (Mobile Intel 4 Series Express Chipset Family).
I confirm that the problem only appears with "Navigation Bar" enabled.
Also, the size or line number of the files to be compared plays a role. I could not figure out an exact limit but the problem occurs at sizes bigger than about 44KB / 7900 lines.
I would be happy to help debugging the problem as I am interested in getting this fixed.