Hmm, this definitely sounds like a bug of some variety. We didn't change this area of the profiler very much in v5, so it's surprising anything has changed
We use the same data for both views so the results should be the same, provided a method is hit only in one place.
If you flip the CPU time drop down back and forth, does the issue go away? I think v5 had a bug where this could get out of sync for the all methods view.
If that doesn't work, which profiling mode are you selecting when this issue occurs?
There's a bug in v6 that occurs when opening results from older profilers that might be the issue you're seeing here. If you click the 'time with children' header in the all methods view to change the sort ordering, do the bar graphs stop lining up with the results?