It's nice for a change to actually see the bug you're trying to help fixing

You're totally right that removing the particle fog is not the right solution as it's just removing the visual symptom of the problem. The root cause is that HD6 didn't care about clamping the values (remember he did the code for himself), so they can go below 0 and/or over 255.
I don't want to post anyone's files mangled by me, but for a quick fix, take the original enbeffect.fx that came with the preset, open enbeffect.fx and scroll down a bit until you see this bit:
Code:
float4 uctcon = float4( 1.00, 1.00, 1.225, 1.025 ); // Contrast Night, Day, v11.2: 1.0, 0.97, 0.85
Lower the night-time contrast (1.225) to 1.0.
The image will become a bit washed out due to loss of contrast, but then scroll down even further (or use search) until you see the post-processing settings of PP2. Find these two lines:
Code:
float EBrightnessV2Night=1.0;
float EBrightnessV2Interior=1.0;
Change both to, say, 0.7. Then find these lines:
Code:
float EIntensityContrastV2Night=1.475;
float EIntensityContrastV2Interior=1.475;
Change both to 1.775.
The image should now look pretty much as intended but without the visual glitches. For exactly similar look you probably need to fine-tune the values a bit.