stilldark&hungry
once issued with an RA a pilot must follow it, even if it contradicts ATC, but when exactly will that happen
Did I misread you... I don't think its difficult to imagine such a scenario? Controller notices two aircraft close together at the same level, acts by issuing a climb clearance to pilot A... but the airborne systems in both aircraft have "co-ordinated" their own avoiding action, giving pilot A a descent instruction, whilst Pilot B is told to climb.
Pilot A is compelled to take the descent.
There are interesting spin-offs too on the subject of TCAS, and at the risk of hi-jacking your point... Eurocontrol recently published a document advising pilots against using ACAS as a total avoidance system. It works vertically, but the display is not optimised for interpretation of the horizontal picture (it gives relative motion, with no indication of actual speed or heading)... There is concern that some pilots are using ACAS/TCAS inappropriately i.e. for separation not limiting it to a collision avoidance tool, and should rely on ATC for that.