It appears that you don't get the achievement for dying to a diggle if it's got a name. My first encounter with a commando diggle was on the 3rd floor, and I got an invisible boss version. When I died (from overestimating myself, mostly), I didn't get the "Be All You Can Be" achievement. I'm guessing the code behind it is looking at the critter's name, and not seeing "Commando Diggle" or whatever it would be.
There are lots of bugs when dealing with dying to things. For example, lots of people have reported that they haven't gotten the one for getting killed by a thrusty. Nobody has the one for Dredmor either.
Some people here said that you get the Thrusty achievement for getting killed by Dredmor, hence you can't get the achievement for getting killed by Dredmor at all.
I have the acheivement for that, granted I got it from a non named diggle commando. So it could well be bugged in the way you mention. On the topic of diggle acheivement bugs - Way of the Dodo is also bugged, at least for me. It has reset about 4 times now, and looking at the amount of people who have the acheivement, seems likely its not just me. Way of the Dodo Kill a thousand Diggles. 6.7% It can be annoying but I am sure they will be fixed (along with more being added). I have faith in the Dev's
Yeah, fun times with Steam achievements: I had my Internet go down for several hours after a thunderstorm; played the game offline using Dredmor.exe and killed Lord Dredmor during the session; never got credit for the kill and even after I got Steam working again it wasn't smart enough to see my "Killed Lord Dredmor" score and award the achievement after the fact. I got killed by Lord Dredmor because I made the mistake of trying to melee him (it was the first time I'd ever encountered him). I ended up with the "Humps" achievement of "being killed by a Thrusty" and no "killed by Dredmor" achievement. Lastly, the "Kill a thousand Diggles" achievement counter has reset or gone down no less than 3 times now; the game claims I have like 500 Diggle kills when it's really more like 1500 and I should have that achievement, too. Good times, good times.