Follow these steps:
1. Close out of any open Diablo processes.
2. Change your d3prefs to settings you want.
3. Launch diablo via normal launcher
4. Verify settings are correct
5. Proceed to launch them via Innerspace
I am guessing you are using innerspace, because I had the same issue when configuring each character d3prefs, so I just set the main one, and launched each character seperately (which copies the d3prefs from the main one).
Yes it is version 44 , after i put read only, the d3prefs.txt file did not change anything, but the prefs for the game went back to the default still.. totally lost....
the culprit strings are PCIVendor and PCIID somewhere near the bottom. They represent your video-card, and if they don't match - it discards the settings and overwrites them. When you paste your d3prefs, make sure to leave the correct IDs (which already exist in current d3prefs after gamelaunch. Also each time you change video-card (if you do) - restore the settings.