What the crap is going on with Dvorak in Carbon apps like Flex Builder and Eclipse :'( very very sad.
It seems that when apps utilise Carbon in Mac OS X 10.5.6 the keyboard mapping reverts to QWERTY instead of dvorak. However, this seems to be only for some keys.
Command+S is still Save
Command+W still closes a window
Command+Q still quits
However, copy and paste are totally screwed.