Having used the VS system of Aircraft Performance, abided by their SOP's and operated for the airline....I can say that this is a rare occurence in VS.
It really sounds to me that there was a breakdown in VS SOP usage on this isolated incident. Simple as that. The crosschecks were ignored/bypassed/not used.
As for Laptop/Computerised speed systems. Well, this is a SORT OF computer system. It is driven through the ACARS system onboard.
I now use a pure Laptop performance system and I must say, it works very well.
But like anything computerised.... Put rubbish in, get rubbish out.
You need to know what you are looking for.