Just got a new JTAGICE3 today, updated the firmware, and tried it with the latest AS5 (5.0.1163). Will not halt at any breakpoints. This has been reported as a problem months ago with the MkII as well. Definitely a problem with AS5 itself.
And this has apparently been going on for months without a patch?
Can anyone suggest an alternate debug environment that works?
One other thing: the JTAGICE3 user guide is pitifully lean. Example: I'm trying to figure out how to single step and use hardware breakpoints and other "advanced" debug features on a mega328p but can't find any direct references. So I'm guessing the 328p/debugWIRE won't support them as they just don't show up in the AS5 menus.