I don't think it's a software problem, rather a "wetware" problem...
I have had a TCAS RA situation where the other pilot did NOTHING in response to the RA. To add complexity to the situation, the ATC controller (in Japan) first gave us a turn away from the traffic, then changed his mind and turned us back into him. Our TCAS gave the appropriate RA, and we avoided him by 700' vertically, with ZERO lateral separation.
In that case there were AT LEAST 2 human errors (not including the one that got him co-altitude on the same airway in the opposite direction in the first place), but the TCAS still gave the appropriate RA advisories. Virtually any deviation from those advisories would have put us back in a collision situation.
To date I have heard of NO events where both pilots followed TCAS RA advisories and still collided with each other or the ground. If you know of any, please provide references.