The ones I embarked (the dead ones) were not, the only miner i have up now is indeed masons. However I thought that the guild bonus of not dying only took effect with harder mining turned on. I guess not then?
I'm going to ask the silly question of, "Did you have Harder Mining turned off when you genned the world?"
Otherwise, the RAWS look fine to me.
In your saved game folder, check the inorganic_zwarpstone.txt file.
You should have various !NOWARP! entries. For example:
!NOWARP!INORGANIC:LIGNITE_DUST]
...
...
...
!NOWARP!INORGANIC:COAL_BITUMINOUS_DUST]
...
...
...
!NOWARP!INORGANIC:ANTHRACITE_DUST]