I have the same problem
I have the exact same issue with my FT-2000 RF Scope, I called Yaesu and they said it sounded like a filter problem on the scope unit board. I was able to fix mine by backing off the drive level on a pot located near the bottom of the board. It stayed fixed for weeks until I moved my setup to another room. I remember setting the drive near the threshold of where it turns back into the white bar accross the screen, perhaps I should have set it less close to that, the reason at the time was the pot linearity was weird and below that threshold the signal peaks were shortened by 40%. and did not look normal until you were right beneath the point where it barred out. I think they are right about the filter, which I think was damaged by a near lightning strike, (200 Yards). I have not re-opened my 2000 to attempt this fine tunning since, when I get the ambition again I hope it works again. Did you ever fix yours?
N2LWN Vinny