Another incident involving TCAS and a loss of separation took place in Canada on 13 July 2001.
The Transportation Safety Board of Canada recently released its final report (A01C0155) and made this finding: "Risk of collision was increased because TCAS and air traffic control are not coordinated. Each flight crew independently decided to disregard the TCAS resolution advisory commands because they were contradictory to instructions the controller had already issued."
The report also said that "On 27 September 2002, Transportation Safety Board sent an Aviation Safety Advisory (615-A020026) to Transport Canada suggesting that they may wish to review current regulations and TCAS guidance material with a view toward developing clear procedures to prevent a risk of collision in the event of conflict between ATC instructions and TCAS RA commands."
This conflict between TCAS commands and ATC instructions is also addressed in FAA Advisory Circular 120-55B which is available in PDF format at this link:
FAA AC 120-55B - Air Carrier Operational Approval and Use of TCAS II
Bottom line? TCAS is the final line of defense. Follow your RA!