Photoshop :: Flattening All Contrast / Where Are Blacks

I edit a photograph from a Camera Raw file to high contrast, grainy black and white, then when I try to flatten it or save it, it washes all the contrast out completely. When I try to merge layers, flatten image or cmd+opt+e/cmd+opt+shift+e to a new file it does the same thing. Here's what I've tried to correct the issue:

-I've tried saving it as a PSD file, a TIFF, a JPEG and a BMP file
-I've tried calibrating my monitor (X-Rite i1 Pro)
-I've tried soft proofing on and off (left off for now)
-I've tried resetting my colour settings to import files into the working space as ProPhoto & Adobe RGB 1998
-I've tried setting the import as the calibrated settings for the screen rather than ProPhoto or Adobe RGB 1998
-I've checked that all files (apart from a Dodge/Burn Layer which has to be on Soft Light never affected any files before) were set to normal
-I've tried converting profiles from ProPhoto to Adobe 1998, Adobe 1998 to sRGB
-I've tried going to preferences in User>Me>Library>Preferences>Adobe Photoshop CS6 Settings and manually resetting all relevant references
-I've tried flushing and resetting all preferences
-I've tried to uninstall and install Photoshop SC6 from scratch
-I've tried restarting the image from the raw file with the new install of CS6, done all the edits again manually...

And it still does the same thing. Whenever I have adjustment layers on my file and have some contrast added that I want to save, it flattens the whole image out..The last attachment is what it looks like in photoshop and another with my colour settings for the (calibrated) screen