Noise on night HDR photos

Ok so I'm doing HDR on night photos, I always keep my iso at 100, and my initial photos don't have noise, but when I put them through Photomatix I get a lot of noise on them, even-though I select the noise reduction setup. Is it because I have an entry model Nikon D5200, or is there a way to avoid it or fix it?

It's probably not noise, they are most likely artifacts generated when the pixels are compressed from the 32bit Radiance file to 16 or 8bit.

You can try turning down the Luminance and/or the Strength slider.

The top 4 sliders and the Lighting Adjustments work on converting the Radiance file into the 16bit file and the 8bit file your screen requires.

You'll find it happens on a lot of images not just those taken in low light. Typical of artifacts it happens most on larger areas of continuous or graduated tones.

It's often better to use a higher ISO in camera and use noise reduction on the files before importing them into Photomatix. Your cameras lowest ISO is not usually the lowest in noise, it differs from sensor to sensor, some experimentation shows it easily, often 400ISO is 'cleaner' than 100 and will certainly be less noisy than lower ISO (some cameras offer 50 or 80).

Here's my HDR set on Flickr, most done with Photomatix