[...]where I frequently hang, crash, or otherwise just have to power cycle the machine[...]
I think this is the key, really. I generally see the errors start to creep in after I have to powercycle the system following a crash. Probably owing to how hard I flog the system, this is often more than once a day.
What driver are you using? (How did you format your CF cards?)
I've been using HDT 2.0.6, mainly out of habit after I ran into so many problems with Lido and A/UX HD SC Setup 3.0.1 being unwilling to write to cards in my PCD-50B card reader. I see in this post
http://68kmla.org/forums/viewtopic.php?p=162316#p162170 from the thread you linked that I'm not the only one who's had stability issues during CF use, so I am heartened that my issues may stem only primarily, rather than completely, from my own incompetence. Unfortunately I don't have a copy of Intech HD SpeedTools, nor is it in my budget for the time being to purchase it, so I think I'm stuck for now.