After days of testing and poring through help files, etc. I've figured out why my quad has been having so many problems. Here it is:
1) APM is arbitrarily changing settings when I use the sub-menus such as "Basic Tuning" "Extended Tuning", etc. Example, if I dare use the "Extended Tuning" configuration tab, it will zero out the Throttle P value to "0". Every time. APM cares not what value is in the board, it will populate that with a "0" in APM and if you dare press "write" it will blow away whatever value was in there before.
2) Each time I disconnect from my Arducopter 2.8 board from my Mac the software will not reconnect, I must restart the software. This isn't a huge problem in and of itself, but it's worth noting.
3) If I dare connect to a PC vs my Mac (I tried that thinking the Mac software was the problem) and it blows away a huge range of settings instantly.
I have no way of knowing if this is an APM software problem inherently, or a problem with my board. But either way it's a massive headache. I've gotten my quad tuned to fly nearly perfectly but extreme care is required to do any tuning. I have to use a snapshot of known good values and if I dare use any configuration dialogs vs. the "Full Config" tool I must compare the before/after values to figure out what's been blown away and screwed up.
Hopefully this is helpful to any others who might be encountering random issues.