Sorry I'm not a Duo owner, so some of my 'help' might be misguided. However, just to get things clear and hopefully to help:
Are you changing the gamma setting (target) in Chromapure? Or is this just the 'base' gamma in the projector? For example I use custom gamma 2.3 as a base for my X35, my target setting was 2.22.
After calibration, try using something like the AVS HD709 test disc:
Find the black full screen test pattern and then adjust the brightness control on the projector down. See if the screen gets any darker. If it does (and especially if you have to adjust a few clicks down before it won't get any darker) then something is wrong in the chain from your player to the Duo and projector.
When you use autocal it is calibrating the output of the Duo to the projector, but you still need to make sure that the Duo's input controls and the player's settings are correctly matched. A simple example might be using HDMI in 'PC' mode (0-255 RGB) which could give elevated blacks if the projector is set to 16-235 RGB. Or another could be that the brightness controls for the Duo's inputs are set too high (I'm assuming it has them like my Lumagen does).
Other set up items to check would be to investigate which colour space setting from your player gives the best result and then make sure that the projector is set to accept this setting (rather than relying on 'auto' which is the default option in JVC menus. Set the JVC HDMI to 'Superwhite' or 'Standard' (the later will limit peak white to 235 the former will allow up to 255 and both will clip below 16 so setting brightness may be slightly harder, though I find '0' is spot on anyway). Set the input to 4:2:2 (or whichever colour space you decide works best with your player and to match the output setting of the Duo) as auto can sometimes select the wrong option, which would usually be obvious with completely 'wrong' colours but could give you raised blacks if using RGB signals and auto decides to select the 'PC' level instead of 'Video RGB' for example.
Make sure that the RGB offsets in the JVC are set to '0' before the autocal. If you increase them above 0 it will raise the black floor and lowering them can cause crushing, so best left alone.
I selected 'Standard' colour space in my X35 which has a slightly oversaturated colour gamut, though I may try 'Wide' next time. If you change this setting you will need to readjust the 100% whitebalance again before re running autocal.
Hope some of this helps.