Have the same problem. With the original wax2.0 Vegas would magically disappear from the screen. With the update it will only disappear intermittently. Extremely frustrating since it is too dangerous to use.
I have been unable to find a common denominator. I can do three or four identical transitions - the first 3 will be fine and then on the fourth - poof - it pulls a David Copperfield.
I found that if I point Wax 2.0b to my Virtual Dub plug-in folder during installation, it will disappear as you describe. There are some incompatible Virtual Dub plug-ins that are causing this behavior, probably the temporal noise reduction filters since they work on more than one frame at a time.