I can confirm this is still an issue in 12.04 release, x64. (Just in case anyone was wondering.)
These should work in the meantime:
caps -> ctrl: setxkbmap -option ctrl:nocaps
caps -> ctrl and Programmer Dvorak: setxkbmap -layout us -variant dvp -option ctrl:nocaps
caps -> ctrl and Programmer Dvorak with inverted numpad: setxkbmap -layout us -variant dvp -option keypad:atm -option ctrl:nocaps
I can confirm this is still an issue in 12.04 release, x64. (Just in case anyone was wondering.)
These should work in the meantime:
caps -> ctrl: setxkbmap -option ctrl:nocaps
caps -> ctrl and Programmer Dvorak: setxkbmap -layout us -variant dvp -option ctrl:nocaps
caps -> ctrl and Programmer Dvorak with inverted numpad: setxkbmap -layout us -variant dvp -option keypad:atm -option ctrl:nocaps